Merge develop to Release_2_8_3_Branch

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index ab50503..3322689 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,29 +1,36 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.io;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
 
+import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -145,6 +152,7 @@ public class FileLoader implements Runnable
   public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
   {
     this.source = source;
+
     file = source.getInFile();
     protocol = source.type;
     this.format = format;
@@ -258,7 +266,7 @@ public class FileLoader implements Runnable
         // load
       }
       loadtime = -System.currentTimeMillis();
-      Alignment al = null;
+      AlignmentI al = null;
 
       if (format.equalsIgnoreCase("Jalview"))
       {
@@ -269,7 +277,7 @@ public class FileLoader implements Runnable
                   .println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
           // We read the data anyway - it might make sense.
         }
-        alignFrame = new Jalview2XML(raiseGUI).LoadJalviewAlign(file);
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
       }
       else
       {
@@ -304,33 +312,56 @@ public class FileLoader implements Runnable
             error = format + "\n" + error;
           }
         }
-        
+
         if ((al != null) && (al.getHeight() > 0))
         {
-          if (viewport != null)
+          for (SequenceI sq : al.getSequences())
           {
-            // TODO: create undo object for this JAL-1101
-            for (int i = 0; i < al.getHeight(); i++)
+            while (sq.getDatasetSequence() != null)
             {
-              viewport.getAlignment().addSequence(al.getSequenceAt(i));
+              sq = sq.getDatasetSequence();
+            }
+            if (sq.getPDBId() != null)
+            {
+              for (PDBEntry pdbe : (List<PDBEntry>) sq.getPDBId())
+              {
+                StructureSelectionManager.getStructureSelectionManager(
+                        Desktop.instance).registerPDBEntry(pdbe);
+              }
             }
-            viewport.firePropertyChange("alignment", null, viewport
-                    .getAlignment().getSequences());
-
+          }
+          if (viewport != null)
+          {
+            viewport.addAlignment(al, title);
           }
           else
           {
             alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
                     AlignFrame.DEFAULT_HEIGHT);
 
-            alignFrame.statusBar.setText("Successfully loaded file "
-                    + title);
+            alignFrame.statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_loaded_file", new String[]
+                    { title }));
 
             if (!protocol.equals(AppletFormatAdapter.PASTE))
+            {
               alignFrame.setFileName(file, format);
+            }
+            if (source instanceof HtmlFile)
+            {
+              ((HtmlFile) source).LoadAlignmentFeatures(alignFrame);
 
-            Desktop.addInternalFrame(alignFrame, title,
-                    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            }
+            if (raiseGUI)
+            {
+              // add the window to the GUI
+              // note - this actually should happen regardless of raiseGUI
+              // status in Jalview 3
+              // TODO: define 'virtual desktop' for benefit of headless scripts
+              // that perform queries to find the 'current working alignment'
+              Desktop.addInternalFrame(alignFrame, title,
+                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            }
 
             try
             {
@@ -357,7 +388,8 @@ public class FileLoader implements Runnable
               public void run()
               {
                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                        errorMessage, "Error loading file",
+                        errorMessage, MessageManager
+                                .getString("label.error_loading_file"),
                         JOptionPane.WARNING_MESSAGE);
               }
             });
@@ -382,8 +414,10 @@ public class FileLoader implements Runnable
           public void run()
           {
             javax.swing.JOptionPane.showInternalMessageDialog(
-                    Desktop.desktop, "Encountered problems opening " + file
-                            + "!!", "File open error",
+                    Desktop.desktop, MessageManager.formatMessage(
+                            "label.problems_opening_file", new String[]
+                            { file }), MessageManager
+                            .getString("label.file_open_error"),
                     javax.swing.JOptionPane.WARNING_MESSAGE);
           }
         });
@@ -403,11 +437,8 @@ public class FileLoader implements Runnable
             javax.swing.JOptionPane
                     .showInternalMessageDialog(
                             Desktop.desktop,
-                            "Out of memory loading file "
-                                    + file
-                                    + "!!"
-                                    + "\nSee help files for increasing Java Virtual Machine memory.",
-                            "Out of memory",
+                            MessageManager.formatMessage("warn.out_of_memory_loading_file", new String[]{file}),
+                            MessageManager.getString("label.out_of_memory"),
                             javax.swing.JOptionPane.WARNING_MESSAGE);
           }
         });