JAL-2446 merged to spike branch

[jalview.git] / src / jalview / gui / VamsasApplication.java

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 4630fd1..d58cb5a 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 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.
  * 
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
@@ -43,7 +44,6 @@ 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;
@@ -174,7 +174,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
           }
         } catch (InvalidSessionDocumentException e)
         {
-          JOptionPane
+          JvOptionPane
                   .showInternalMessageDialog(
                           Desktop.desktop,
 
@@ -182,7 +182,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                                   .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
                           MessageManager
                                   .getString("label.vamsas_document_import_failed"),
-                          JOptionPane.ERROR_MESSAGE);
+                          JvOptionPane.ERROR_MESSAGE);
 
         }
       }
@@ -321,6 +321,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     Thread udthread = new Thread(new Runnable()
     {
 
+      @Override
       public void run()
       {
         Cache.log.info("Jalview updating to the Vamsas Session.");
@@ -639,6 +640,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     final VamsasApplication client = this;
     vclient.addDocumentUpdateHandler(new PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
         Cache.log.debug("Dealing with document update event.");
@@ -656,21 +658,22 @@ public class VamsasApplication implements SelectionSource, VamsasSource
             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
+                  int reply = JvOptionPane
                           .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);
+                                  JvOptionPane.YES_NO_OPTION,
+                                  JvOptionPane.QUESTION_MESSAGE);
 
-                  if (reply == JOptionPane.YES_OPTION)
+                  if (reply == JvOptionPane.YES_OPTION)
                   {
                     Cache.log.debug("Prompting for vamsas store filename.");
                     Desktop.instance.vamsasSave_actionPerformed(null);
@@ -774,6 +777,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         {
           String last = null;
 
+          @Override
           public void handleMessage(Message message)
           {
             if (vobj2jv == null)
@@ -817,7 +821,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               {
                 // 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;
@@ -951,7 +955,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               }
               if (send)
               {
-                ssm.sendSelection(jselection, colsel, me);
+                ssm.sendSelection(jselection, colsel, null, me);
               }
               // discard message.
               for (int c = 0; c < jvobjs.length; c++)
@@ -998,8 +1002,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         selecter = new SelectionListener()
         {
 
+          @Override
           public void selection(SequenceGroup seqsel,
-                  ColumnSelection colsel, SelectionSource source)
+                  ColumnSelection colsel, HiddenColumns hidden,
+                  SelectionSource source)
           {
             if (vobj2jv == null)
             {
@@ -1065,17 +1071,18 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   {
                     // gather selected columns outwith the sequence positions
                     // too
-                    for (Object obj : colsel.getSelected())
+                    for (Integer ival : colsel.getSelected())
                     {
-                      int ival = ((Integer) obj).intValue();
                       Pos p = new Pos();
-                      p.setI(ival + 1);
+                      p.setI(ival.intValue() + 1);
                       range.addPos(p);
                     }
                   }
                   else
                   {
-                    int[] intervals = colsel.getVisibleContigs(
+                    // int[] intervals = colsel.getVisibleContigs(
+                    // seqsel.getStartRes(), seqsel.getEndRes() + 1);
+                    int[] intervals = hidden.getVisibleContigs(
                             seqsel.getStartRes(), seqsel.getEndRes() + 1);
                     for (int iv = 0; iv < intervals.length; iv += 2)
                     {