/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.io;
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Jalview;
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.json.binding.biojson.v1.ColourSchemeMapper;
+import jalview.schemes.ColourSchemeI;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
import java.util.StringTokenizer;
import java.util.Vector;
-import jalview.util.MessageManager;
import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
{
this.source = source;
+
file = source.getInFile();
protocol = source.type;
this.format = format;
{
format = new IdentifyFile().Identify(file, protocol);
}
+
+ }
+
+ if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+ {
+ Desktop.instance.stopLoading();
+ System.err.println("The input file \"" + file
+ + "\" has null or unidentifiable data content!");
+ if (!Jalview.isHeadlessMode())
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.couldnt_read_data")
+ + " in " + file + "\n"
+ + AppletFormatAdapter.SUPPORTED_FORMATS,
+ MessageManager.getString("label.couldnt_read_data"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ return;
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
// retrieved via URL)
.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 ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
{
- if (viewport != null)
+ // construct and register dataset sequences
+ 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)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ if (sq.getAllPDBEntries() != null)
{
- viewport.getAlignment().addSequence(al.getSequenceAt(i));
+ for (PDBEntry pdbe : sq.getAllPDBEntries())
+ {
+ // register PDB entries with desktop's structure selection
+ // manager
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(pdbe);
+ }
}
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ }
+
+ if (viewport != null)
+ {
+ // append to existing alignment
+ viewport.addAlignment(al, title);
}
else
{
- alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ // otherwise construct the alignFrame
- alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new String[]
- { title }));
+ if (source instanceof ComplexAlignFile)
+ {
+ ColumnSelection colSel = ((ComplexAlignFile) source)
+ .getColumnSelection();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ boolean showSeqFeatures = ((ComplexAlignFile) source)
+ .isShowSeqFeatures();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+ .getDisplayedFeatures();
+ alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ alignFrame.getViewport().setShowSequenceFeatures(
+ showSeqFeatures);
+ alignFrame.getViewport().setFeaturesDisplayed(fd);
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ 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
Desktop.instance.stopLoading();
}
- final String errorMessage = "Couldn't load file " + title + "\n"
- + error;
- if (raiseGUI)
+ final String errorMessage = MessageManager
+ .getString("label.couldnt_load_file")
+ + " "
+ + title
+ + "\n" + error;
+ // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
+ // bits ?
+ if (raiseGUI && Desktop.desktop != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
{
javax.swing.JOptionPane.showInternalMessageDialog(
Desktop.desktop, MessageManager.formatMessage(
- "label.problems_opening_file", new String[]
- { file }), MessageManager
+ "label.problems_opening_file",
+ new String[] { file }), MessageManager
.getString("label.file_open_error"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
{
public void run()
{
- javax.swing.JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.formatMessage("warn.out_of_memory_loading_file", new String[]{file}),
- MessageManager.getString("label.out_of_memory"),
- javax.swing.JOptionPane.WARNING_MESSAGE);
+ javax.swing.JOptionPane.showInternalMessageDialog(
+ Desktop.desktop, MessageManager.formatMessage(
+ "warn.out_of_memory_loading_file", new String[]
+ { file }), MessageManager
+ .getString("label.out_of_memory"),
+ javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
}
git://source.jalview.org / jalview.git / blobdiff