Merge branch 'develop' into features/JAL-653_gffalignments

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 82b94c3..7387fa2 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -20,17 +20,19 @@
  */
 package jalview.io;
 
+import jalview.api.ComplexAlignFile;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 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.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
-import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -152,6 +154,7 @@ public class FileLoader implements Runnable
   public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
   {
     this.source = source;
+
     file = source.getInFile();
     protocol = source.type;
     this.format = format;
@@ -276,7 +279,7 @@ 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
       {
@@ -296,7 +299,7 @@ public class FileLoader implements Runnable
               // open a new source and read from it
               FormatAdapter fa = new FormatAdapter();
               al = fa.readFile(file, protocol, format);
-              source = fa.afile; // keep reference for later if necessary.
+              source = fa.getAlignFile(); // keep reference for later if necessary.
             }
           } catch (java.io.IOException ex)
           {
@@ -314,6 +317,7 @@ public class FileLoader implements Runnable
 
         if ((al != null) && (al.getHeight() > 0))
         {
+          // construct and register dataset sequences
           for (SequenceI sq : al.getSequences())
           {
             while (sq.getDatasetSequence() != null)
@@ -322,55 +326,76 @@ public class FileLoader implements Runnable
             }
             if (sq.getPDBId() != null)
             {
-              for (PDBEntry pdbe : (List<PDBEntry>) sq.getPDBId())
+              for (PDBEntry pdbe : sq.getPDBId())
               {
+                // register PDB entries with desktop's structure selection
+                // manager
                 StructureSelectionManager.getStructureSelectionManager(
                         Desktop.instance).registerPDBEntry(pdbe);
               }
             }
           }
+
           if (viewport != null)
           {
-            // TODO: create undo object for this JAL-1101
-            for (int i = 0; i < al.getHeight(); i++)
-            {
-              viewport.getAlignment().addSequence(al.getSequenceAt(i));
-            }
-            viewport.firePropertyChange("alignment", null, viewport
-                    .getAlignment().getSequences());
+            // append to existing alignment
+            viewport.addAlignment(al, title);
           }
           else
           {
-            alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-                    AlignFrame.DEFAULT_HEIGHT);
-
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
-                    "label.successfully_loaded_file", new String[]
-                    { title }));
+            // otherwise construct the alignFrame
 
-            if (!protocol.equals(AppletFormatAdapter.PASTE))
-            {
-              alignFrame.setFileName(file, format);
-            }
-            if (raiseGUI)
+            if (source instanceof ComplexAlignFile)
             {
-              // 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,
+              ColumnSelection colSel = ((ComplexAlignFile) source)
+                      .getColumnSelection();
+              SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                      .getHiddenSequences();
+              boolean showSeqFeatures = ((ComplexAlignFile) source)
+                      .isShowSeqFeatures();
+              ColourSchemeI cs = ((ComplexAlignFile) source)
+                      .getColourScheme();
+              alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-            }
 
-            try
-            {
-              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
-                      "SHOW_FULLSCREEN", false));
-            } catch (java.beans.PropertyVetoException ex)
+              alignFrame.getViewport().setShowSequenceFeatures(
+                      showSeqFeatures);
+              alignFrame.changeColour(cs);
+            }
+            else
             {
+              alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                      AlignFrame.DEFAULT_HEIGHT);
             }
           }
+          // add metadata and update ui
+          if (!protocol.equals(AppletFormatAdapter.PASTE))
+          {
+            alignFrame.setFileName(file, format);
+          }
+
+          alignFrame.statusBar.setText(MessageManager.formatMessage(
+                  "label.successfully_loaded_file", new String[]
+                  { title }));
+
+          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
+          {
+            alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+                    "SHOW_FULLSCREEN", false));
+          } catch (java.beans.PropertyVetoException ex)
+          {
+          }
         }
         else
         {
@@ -381,7 +406,9 @@ public class FileLoader implements Runnable
 
           final String errorMessage = "Couldn't load file " + title + "\n"
                   + error;
-          if (raiseGUI)
+          // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
+          // bits ?
+          if (raiseGUI && Desktop.desktop != null)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {