/*
- * 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.
*
*/
package jalview.io;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+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 java.util.StringTokenizer;
-import java.util.Vector;
-
+import jalview.schemes.ColourSchemeI;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
{
this.source = source;
+
file = source.getInFile();
protocol = source.type;
this.format = format;
.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
{
// 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)
{
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();
}
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
-
+ if (sq.getPDBId() != null)
+ {
+ for (PDBEntry pdbe : sq.getPDBId())
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(pdbe);
+ }
+ }
+ }
+ if (viewport != null)
+ {
+ viewport.addAlignment(al, title);
}
else
{
- alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ if (!protocol.equals(AppletFormatAdapter.PASTE))
+ {
+ alignFrame.setFileName(file, format);
+ }
+ if (source instanceof ComplexAlignFile)
+ {
+ 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);
+
+ alignFrame.getViewport().setShowSequenceFeatures(
+ showSeqFeatures);
+ alignFrame.changeColour(cs);
+ }
+ else
+ {
+ alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
alignFrame.statusBar.setText(MessageManager.formatMessage(
"label.successfully_loaded_file", new String[]
{ title }));
- if (!protocol.equals(AppletFormatAdapter.PASTE))
- alignFrame.setFileName(file, format);
if (raiseGUI)
{
// add the window to the GUI
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);
}
});