X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=dabec6d6e8eb5a8c51c2565a6496b6e6cf3a7442;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=efd94de08b633823ace20430cba4ff1886c3bc87;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index efd94de..dabec6d 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,25 +1,30 @@
 /*
- * 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 ($$Version-Rel$$)
+ * 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.gui;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
@@ -27,24 +32,24 @@ import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasListener;
+import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.io.File;
 import java.io.IOException;
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
 
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 
 import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.IClient;
 import uk.ac.vamsas.client.IClientDocument;
 import uk.ac.vamsas.client.InvalidSessionDocumentException;
-import uk.ac.vamsas.client.NoDefaultSessionException;
 import uk.ac.vamsas.client.UserHandle;
 import uk.ac.vamsas.client.VorbaId;
 import uk.ac.vamsas.client.picking.IMessageHandler;
@@ -61,7 +66,7 @@ import uk.ac.vamsas.objects.core.Seg;
  * @author jimp
  * 
  */
-public class VamsasApplication implements SelectionSource
+public class VamsasApplication implements SelectionSource, VamsasSource
 {
   IClient vclient = null;
 
@@ -152,8 +157,8 @@ public class VamsasApplication implements SelectionSource
       {
         if (sess != null)
         {
-          throw new Error(
-                  "Implementation Error - cannot import existing vamsas document into an existing session, Yet!");
+          throw new Error(MessageManager.getString(
+                  "error.implementation_error_cannot_import_vamsas_doc"));
         }
         try
         {
@@ -169,13 +174,13 @@ public class VamsasApplication implements SelectionSource
           }
         } catch (InvalidSessionDocumentException e)
         {
-          JOptionPane
-                  .showInternalMessageDialog(
-                          Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 
-                          "VAMSAS Document could not be opened as a new session - please choose another",
-                          "VAMSAS Document Import Failed",
-                          JOptionPane.ERROR_MESSAGE);
+                  MessageManager.getString(
+                          "label.vamsas_doc_couldnt_be_opened_as_new_session"),
+                  MessageManager
+                          .getString("label.vamsas_document_import_failed"),
+                  JvOptionPane.ERROR_MESSAGE);
 
         }
       }
@@ -197,8 +202,7 @@ public class VamsasApplication implements SelectionSource
 
     } catch (Exception e)
     {
-      jalview.bin.Cache.log
-              .error("Couldn't instantiate vamsas client !", e);
+      Console.error("Couldn't instantiate vamsas client !", e);
       return false;
     }
     return true;
@@ -221,14 +225,14 @@ public class VamsasApplication implements SelectionSource
       }
     } catch (Error e)
     {
-      Cache.log
-              .warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
-                      e);
+      Console.warn(
+              "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
+              e);
     } catch (Exception e)
     {
-      Cache.log
-              .warn("Probable VAMSAS client incompatibility - carrying on regardless",
-                      e);
+      Console.warn(
+              "Probable VAMSAS client incompatibility - carrying on regardless",
+              e);
     }
   }
 
@@ -240,7 +244,7 @@ public class VamsasApplication implements SelectionSource
   private ClientHandle getJalviewHandle()
   {
     return new ClientHandle("jalview.bin.Jalview",
-            jalview.bin.Cache.getProperty("VERSION"));
+            Cache.getProperty("VERSION"));
   }
 
   /**
@@ -261,18 +265,17 @@ public class VamsasApplication implements SelectionSource
     if (!inSession())
     {
       throw new Error(
-              "Impementation error! Vamsas Operations when client not initialised and connected.");
+              "Implementation error! Vamsas Operations when client not initialised and connected");
     }
     addDocumentUpdateHandler();
     addStoreDocumentHandler();
     startSession();
     inInitialUpdate = true;
-    Cache.log
-            .debug("Jalview loading the Vamsas Session for the first time.");
+    Console.debug("Jalview loading the Vamsas Session for the first time.");
     dealWithDocumentUpdate(false); // we don't push an update out to the
     inInitialUpdate = false;
     // document yet.
-    Cache.log.debug("... finished update for the first time.");
+    Console.debug("... finished update for the first time.");
   }
 
   /**
@@ -302,9 +305,9 @@ public class VamsasApplication implements SelectionSource
       }
     } catch (Exception e)
     {
-      Cache.log
-              .warn("Exception whilst refreshing jalview windows after a vamsas document update.",
-                      e);
+      Console.warn(
+              "Exception whilst refreshing jalview windows after a vamsas document update.",
+              e);
     }
   }
 
@@ -313,15 +316,16 @@ public class VamsasApplication implements SelectionSource
     Thread udthread = new Thread(new Runnable()
     {
 
+      @Override
       public void run()
       {
-        Cache.log.info("Jalview updating to the Vamsas Session.");
+        Console.info("Jalview updating to the Vamsas Session.");
 
         dealWithDocumentUpdate(true);
-        Cache.log.info("Jalview finished updating to the Vamsas Session.");
+        Console.info("Jalview finished updating to the Vamsas Session.");
       }
 
-    });
+    }, "UpdateVamsas");
     udthread.start();
   }
 
@@ -345,8 +349,10 @@ public class VamsasApplication implements SelectionSource
   public void end_session(boolean promptUser)
   {
     if (!inSession())
-      throw new Error("Jalview not connected to Vamsas session.");
-    Cache.log.info("Jalview disconnecting from the Vamsas Session.");
+    {
+      throw new Error("Jalview not connected to Vamsas session");
+    }
+    Console.info("Jalview disconnecting from the Vamsas Session.");
     try
     {
       if (joinedSession)
@@ -354,13 +360,13 @@ public class VamsasApplication implements SelectionSource
         boolean ourprompt = this.promptUser;
         this.promptUser = promptUser;
         vclient.finalizeClient();
-        Cache.log.info("Jalview has left the session.");
+        Console.info("Jalview has left the session.");
         this.promptUser = ourprompt; // restore default value
       }
       else
       {
-        Cache.log
-                .warn("JV Client leaving a session that's its not joined yet.");
+        Console.warn(
+                "JV Client leaving a session that's its not joined yet.");
       }
       joinedSession = false;
       vclient = null;
@@ -370,13 +376,13 @@ public class VamsasApplication implements SelectionSource
       vobj2jv = null;
     } catch (Exception e)
     {
-      Cache.log.error("Vamsas Session finalization threw exceptions!", e);
+      Console.error("Vamsas Session finalization threw exceptions!", e);
     }
   }
 
   public void updateJalview(IClientDocument cdoc)
   {
-    Cache.log.debug("Jalview updating from sesion document ..");
+    Console.debug("Jalview updating from sesion document ..");
     ensureJvVamsas();
     VamsasAppDatastore vds = new VamsasAppDatastore(cdoc, vobj2jv, jv2vobj,
             baseProvEntry(), alRedoState);
@@ -385,7 +391,7 @@ public class VamsasApplication implements SelectionSource
       vds.updateToJalview();
     } catch (Exception e)
     {
-      Cache.log.error("Failed to update Jalview from vamsas document.", e);
+      Console.error("Failed to update Jalview from vamsas document.", e);
     }
     try
     {
@@ -397,10 +403,10 @@ public class VamsasApplication implements SelectionSource
       }
     } catch (Exception e)
     {
-      Cache.log.error(
+      Console.error(
               "Exception when updating Jalview settings from Appdata.", e);
     }
-    Cache.log.debug(".. finished updating from sesion document.");
+    Console.debug(".. finished updating from sesion document.");
 
   }
 
@@ -474,11 +480,9 @@ public class VamsasApplication implements SelectionSource
             } catch (Exception e)
             {
               errorsDuringUpdate = true;
-              Cache.log.error("Exception synchronizing "
-                      + af.getTitle()
-                      + " "
-                      + (af.getViewport().viewName == null ? "" : " view "
-                              + af.getViewport().viewName)
+              Console.error("Exception synchronizing " + af.getTitle() + " "
+                      + (af.getViewport().getViewName() == null ? ""
+                              : " view " + af.getViewport().getViewName())
                       + " to document.", e);
               stored = false;
             }
@@ -513,7 +517,7 @@ public class VamsasApplication implements SelectionSource
       }
     } catch (Exception e)
     {
-      Cache.log.error("Exception synchronizing Views to Document :", e);
+      Console.error("Exception synchronizing Views to Document :", e);
       errorsDuringUpdate = true;
     }
 
@@ -530,7 +534,7 @@ public class VamsasApplication implements SelectionSource
       }
     } catch (Exception e)
     {
-      Cache.log.error("Client Appdata Write exception", e);
+      Console.error("Client Appdata Write exception", e);
       errorsDuringAppUpdate = true;
     }
     vds.clearSkipList();
@@ -558,32 +562,32 @@ public class VamsasApplication implements SelectionSource
   {
     int storedviews = 0;
     // called by update handler for document update.
-    Cache.log.debug("Updating jalview from changed vamsas document.");
+    Console.debug("Updating jalview from changed vamsas document.");
     disableGui(true);
     try
     {
       long time = System.currentTimeMillis();
       IClientDocument cdoc = vclient.getClientDocument();
-      if (Cache.log.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        Cache.log.debug("Time taken to get ClientDocument = "
+        Console.debug("Time taken to get ClientDocument = "
                 + (System.currentTimeMillis() - time));
         time = System.currentTimeMillis();
       }
       if (fromJalview)
       {
         storedviews += updateVamsasDocument(cdoc);
-        if (Cache.log.isDebugEnabled())
+        if (Console.isDebugEnabled())
         {
-          Cache.log
-                  .debug("Time taken to update Vamsas Document from jalview\t= "
+          Console.debug(
+                  "Time taken to update Vamsas Document from jalview\t= "
                           + (System.currentTimeMillis() - time));
           time = System.currentTimeMillis();
         }
         cdoc.setVamsasRoots(cdoc.getVamsasRoots());
-        if (Cache.log.isDebugEnabled())
+        if (Console.isDebugEnabled())
         {
-          Cache.log.debug("Time taken to set Document Roots\t\t= "
+          Console.debug("Time taken to set Document Roots\t\t= "
                   + (System.currentTimeMillis() - time));
           time = System.currentTimeMillis();
         }
@@ -591,19 +595,19 @@ public class VamsasApplication implements SelectionSource
       else
       {
         updateJalview(cdoc);
-        if (Cache.log.isDebugEnabled())
+        if (Console.isDebugEnabled())
         {
-          Cache.log
-                  .debug("Time taken to update Jalview from vamsas document Roots\t= "
+          Console.debug(
+                  "Time taken to update Jalview from vamsas document Roots\t= "
                           + (System.currentTimeMillis() - time));
           time = System.currentTimeMillis();
         }
 
       }
       vclient.updateDocument(cdoc);
-      if (Cache.log.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        Cache.log.debug("Time taken to update Session Document\t= "
+        Console.debug("Time taken to update Session Document\t= "
                 + (System.currentTimeMillis() - time));
         time = System.currentTimeMillis();
       }
@@ -617,7 +621,7 @@ public class VamsasApplication implements SelectionSource
       recover_objectMappingBackup();
       storedviews = 0;
     }
-    Cache.log.debug("Finished updating from document change.");
+    Console.debug("Finished updating from document change.");
     disableGui(false);
     return storedviews;
   }
@@ -627,14 +631,15 @@ public class VamsasApplication implements SelectionSource
     final VamsasApplication client = this;
     vclient.addDocumentUpdateHandler(new PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
-        Cache.log.debug("Dealing with document update event.");
+        Console.debug("Dealing with document update event.");
         client.dealWithDocumentUpdate(false);
-        Cache.log.debug("finished dealing with event.");
+        Console.debug("finished dealing with event.");
       }
     });
-    Cache.log.debug("Added Jalview handler for vamsas document updates.");
+    Console.debug("Added Jalview handler for vamsas document updates.");
   }
 
   private void addStoreDocumentHandler()
@@ -644,43 +649,43 @@ public class VamsasApplication implements SelectionSource
             uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE,
             new PropertyChangeListener()
             {
+              @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
                 if (client.promptUser)
                 {
-                  Cache.log
-                          .debug("Asking user if the vamsas session should be stored.");
-                  int reply = JOptionPane
-                          .showInternalConfirmDialog(
-                                  Desktop.desktop,
-                                  "The current VAMSAS session has unsaved data - do you want to save it ?",
-                                  "VAMSAS Session Shutdown",
-                                  JOptionPane.YES_NO_OPTION,
-                                  JOptionPane.QUESTION_MESSAGE);
-
-                  if (reply == JOptionPane.YES_OPTION)
+                  Console.debug(
+                          "Asking user if the vamsas session should be stored.");
+                  int reply = JvOptionPane.showInternalConfirmDialog(
+                          Desktop.desktop,
+                          "The current VAMSAS session has unsaved data - do you want to save it ?",
+                          "VAMSAS Session Shutdown",
+                          JvOptionPane.YES_NO_OPTION,
+                          JvOptionPane.QUESTION_MESSAGE);
+
+                  if (reply == JvOptionPane.YES_OPTION)
                   {
-                    Cache.log.debug("Prompting for vamsas store filename.");
+                    Console.debug("Prompting for vamsas store filename.");
                     Desktop.instance.vamsasSave_actionPerformed(null);
-                    Cache.log
-                            .debug("Finished attempt at storing document.");
+                    Console.debug("Finished attempt at storing document.");
                   }
-                  Cache.log
-                          .debug("finished dealing with REQUESTTOCLOSE event.");
+                  Console.debug(
+                          "finished dealing with REQUESTTOCLOSE event.");
                 }
                 else
                 {
-                  Cache.log
-                          .debug("Ignoring store document request (promptUser==false)");
+                  Console.debug(
+                          "Ignoring store document request (promptUser==false)");
                 }
               }
             });
-    Cache.log.debug("Added Jalview handler for vamsas document updates.");
+    Console.debug("Added Jalview handler for vamsas document updates.");
   }
 
   public void disableGui(boolean b)
   {
-    Desktop.instance.setVamsasUpdate(b);
+    // JAL-3311 TODO: remove this class!
+    // Desktop.instance.setVamsasUpdate(b);
   }
 
   Hashtable _backup_vobj2jv;
@@ -714,7 +719,7 @@ public class VamsasApplication implements SelectionSource
       }
 
       throw new Error(
-              "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made.");
+              "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made");
     }
     jv2vobj.clear();
     Iterator el = _backup_jv2vobj.entrySet().iterator();
@@ -748,19 +753,20 @@ public class VamsasApplication implements SelectionSource
       } catch (Exception e)
       {
         // Complain to GUI
-        Cache.log.error("Failed to join vamsas session.", e);
+        Console.error("Failed to join vamsas session.", e);
         vclient = null;
       }
       try
       {
         final IPickManager pm = vclient.getPickManager();
         final StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager();
-        final SelectionSource me = this;
+                .getStructureSelectionManager(Desktop.instance);
+        final VamsasApplication me = this;
         pm.registerMessageHandler(new IMessageHandler()
         {
           String last = null;
 
+          @Override
           public void handleMessage(Message message)
           {
             if (vobj2jv == null)
@@ -776,20 +782,20 @@ public class VamsasApplication implements SelectionSource
               {
                 return;
               }
-              // if (Cache.log.isDebugEnabled())
+              // if (Cache.isDebugEnabled())
               // {
-              // Cache.log.debug("Received MouseOverMessage "+mm.getVorbaID()+"
+              // Cache.debug("Received MouseOverMessage "+mm.getVorbaID()+"
               // "+mm.getPosition());
               // }
               Object jvobj = vobj2jv.get(mm.getVorbaID());
               if (jvobj != null && jvobj instanceof SequenceI)
               {
                 last = mstring;
-                // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
+                // Cache.debug("Handling Mouse over "+mm.getVorbaID()+"
                 // bound to "+jvobj+" at "+mm.getPosition());
                 // position is character position in aligned sequence
                 ssm.mouseOverVamsasSequence((SequenceI) jvobj,
-                        mm.getPosition());
+                        mm.getPosition(), me);
               }
             }
             if (message instanceof uk.ac.vamsas.client.picking.SelectionMessage)
@@ -804,7 +810,7 @@ public class VamsasApplication implements SelectionSource
               {
                 // TODO: rationalise : can only clear a selection over a
                 // referred to object
-                ssm.sendSelection(null, null, me);
+                ssm.sendSelection(null, null, null, me);
                 return;
               }
               Class type = null;
@@ -920,8 +926,8 @@ public class VamsasApplication implements SelectionSource
                       {
                         jselection.setStartRes(prange[p + l] - 1);
                       }
-                      if (jselection.getEndRes() <= maxWidth
-                              && prange[p + u] == (jselection.getEndRes() + 2))
+                      if (jselection.getEndRes() <= maxWidth && prange[p
+                              + u] == (jselection.getEndRes() + 2))
                       {
                         jselection.setEndRes(prange[p + u] - 1);
                       }
@@ -938,7 +944,7 @@ public class VamsasApplication implements SelectionSource
               }
               if (send)
               {
-                ssm.sendSelection(jselection, colsel, me);
+                ssm.sendSelection(jselection, colsel, null, me);
               }
               // discard message.
               for (int c = 0; c < jvobjs.length; c++)
@@ -957,17 +963,21 @@ public class VamsasApplication implements SelectionSource
 
           int i = -1;
 
-          public void mouseOver(SequenceI seq, int index)
+          @Override
+          public void mouseOverSequence(SequenceI seq, int index,
+                  VamsasSource source)
           {
             if (jv2vobj == null)
+            {
               return;
+            }
             if (seq != last || i != index)
             {
               VorbaId v = (VorbaId) jv2vobj.get(seq);
               if (v != null)
               {
                 // this should really be a trace message.
-                // Cache.log.debug("Mouse over " + v.getId() + " bound to "
+                // Cache.debug("Mouse over " + v.getId() + " bound to "
                 // + seq + " at " + index);
                 last = seq;
                 i = index;
@@ -981,13 +991,15 @@ public class VamsasApplication implements SelectionSource
         selecter = new SelectionListener()
         {
 
+          @Override
           public void selection(SequenceGroup seqsel,
-                  ColumnSelection colsel, SelectionSource source)
+                  ColumnSelection colsel, HiddenColumns hidden,
+                  SelectionSource source)
           {
             if (vobj2jv == null)
             {
-              Cache.log
-                      .warn("Selection listener still active for dead session.");
+              Console.warn(
+                      "Selection listener still active for dead session.");
               // not in a session.
               return;
             }
@@ -996,19 +1008,21 @@ public class VamsasApplication implements SelectionSource
               AlignmentI visal = null;
               if (source instanceof AlignViewport)
               {
-                visal = ((AlignViewport) source).getAlignment();
+                visal = ((AlignmentViewport) source).getAlignment();
               }
               SelectionMessage sm = null;
               if ((seqsel == null || seqsel.getSize() == 0)
-                      && (colsel == null || colsel.getSelected() == null || colsel
-                              .getSelected().size() == 0))
+                      && (colsel == null || colsel.getSelected() == null
+                              || colsel.getSelected().size() == 0))
               {
                 if (source instanceof AlignViewport)
                 {
                   // the empty selection.
-                  sm = new SelectionMessage("jalview", new String[]
-                  { ((AlignViewport) source).getSequenceSetId() }, null,
-                          true);
+                  sm = new SelectionMessage("jalview",
+                          new String[]
+                          { ((AlignmentViewport) source)
+                                  .getSequenceSetId() },
+                          null, true);
                 }
                 else
                 {
@@ -1020,10 +1034,8 @@ public class VamsasApplication implements SelectionSource
               {
                 String[] vobj = new String[seqsel.getSize()];
                 int o = 0;
-                Enumeration sels = seqsel.getSequences(null).elements();
-                while (sels.hasMoreElements())
+                for (SequenceI sel : seqsel.getSequences(null))
                 {
-                  SequenceI sel = (SequenceI) sels.nextElement();
                   VorbaId v = (VorbaId) jv2vobj.get(sel);
                   if (v != null)
                   {
@@ -1050,25 +1062,25 @@ public class VamsasApplication implements SelectionSource
                   {
                     // gather selected columns outwith the sequence positions
                     // too
-                    Enumeration cols = colsel.getSelected().elements();
-                    while (cols.hasMoreElements())
+                    for (Integer ival : colsel.getSelected())
                     {
-                      int ival = ((Integer) cols.nextElement()).intValue();
                       Pos p = new Pos();
-                      p.setI(ival + 1);
+                      p.setI(ival.intValue() + 1);
                       range.addPos(p);
                     }
                   }
                   else
                   {
-                    int[] intervals = colsel.getVisibleContigs(
-                            seqsel.getStartRes(), seqsel.getEndRes() + 1);
-                    for (int iv = 0; iv < intervals.length; iv += 2)
+                    Iterator<int[]> intervals = hidden
+                            .getVisContigsIterator(seqsel.getStartRes(),
+                                    seqsel.getEndRes() + 1, false);
+                    while (intervals.hasNext())
                     {
+                      int[] region = intervals.next();
                       Seg s = new Seg();
-                      s.setStart(intervals[iv] + 1); // vamsas indices begin at
-                      // 1, not zero.
-                      s.setEnd(intervals[iv + 1] + 1);
+                      s.setStart(region[0] + 1); // vamsas indices begin at 1,
+                                                 // not zero.
+                      s.setEnd(region[1] + 1);
                       s.setInclusive(true);
                       range.addSeg(s);
                     }
@@ -1086,7 +1098,7 @@ public class VamsasApplication implements SelectionSource
               if (sm != null)
               {
                 sm.validate(); // debug
-                Cache.log.debug("Selection Message\n" + sm.getRawMessage());
+                Console.debug("Selection Message\n" + sm.getRawMessage());
                 pm.sendMessage(sm);
               }
             }
@@ -1097,7 +1109,7 @@ public class VamsasApplication implements SelectionSource
         ssm.addSelectionListener(selecter);
       } catch (Exception e)
       {
-        Cache.log.error("Failed to init Vamsas Picking", e);
+        Console.error("Failed to init Vamsas Picking", e);
       }
     }
   }