/*
- * 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)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.api.ComplexAlignFile;
import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
{
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)
}
}
- if ((al != null) && (al.getHeight() > 0))
+ if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
{
// construct and register dataset sequences
for (SequenceI sq : al.getSequences())
{
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
}
alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new String[]
- { title }));
+ "label.successfully_loaded_file",
+ new String[] { title }));
if (raiseGUI)
{
Desktop.instance.stopLoading();
}
- final String errorMessage = "Couldn't load file " + title + "\n"
- + error;
+ 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.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);
}