/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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 java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
-
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.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 javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
public class FileLoader implements Runnable
{
String file;
{
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)
// open a new source and read from it
FormatAdapter fa = new FormatAdapter();
al = fa.readFile(file, protocol, format);
- source = fa.getAlignFile(); // 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())
{
+ // construct and register dataset sequences
for (SequenceI sq : al.getSequences())
{
while (sq.getDatasetSequence() != null)
{
sq = sq.getDatasetSequence();
}
- if (sq.getPDBId() != null)
+ if (sq.getAllPDBEntries() != null)
{
- for (PDBEntry pdbe : sq.getPDBId())
+ for (PDBEntry pdbe : sq.getAllPDBEntries())
{
+ // register PDB entries with desktop's structure selection
+ // manager
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(pdbe);
}
}
}
+
if (viewport != null)
{
+ // append to existing alignment
viewport.addAlignment(al, title);
}
else
.getHiddenSequences();
boolean showSeqFeatures = ((ComplexAlignFile) source)
.isShowSeqFeatures();
- ColourSchemeI cs = ((ComplexAlignFile) source)
- .getColourScheme();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+ .getDisplayedFeatures();
alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
alignFrame.getViewport().setShowSequenceFeatures(
showSeqFeatures);
- alignFrame.changeColour(cs);
+ 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);
- }
+ // 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 }));
+ 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);
- }
+ 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)
- {
+ try
+ {
+ alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
}
}
else
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