import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
+import jalview.gui.BamFileOptionsChooser;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.ws.utils.UrlDownloadClient;
+import java.io.File;
+import java.io.IOException;
import java.util.StringTokenizer;
import java.util.Vector;
-import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
FileFormatI format;
- AlignmentFileI source = null; // alternative specification of where data comes
+ AlignmentFileReaderI source = null; // alternative specification of where data
+ // comes
// from
* @param format
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source,
+ public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
FileFormatI format)
{
this.source = source;
// refer to it as.
return;
}
+ if (file != null
+ && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+ {
+ // ignore files loaded from the system's temporary directory
+ return;
+ }
String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
: "RECENT_URL";
if (protocol == DataSourceType.FILE)
{
- Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString());
+ Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
}
}
@Override
public void run()
{
- String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
+ String title = protocol == DataSourceType.PASTE
+ ? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
try
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
- javax.swing.JOptionPane.showInternalMessageDialog(
- Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
- + AppletFormatAdapter.SUPPORTED_FORMATS,
+ + AppletFormatAdapter.getSupportedFormats(),
MessageManager.getString("label.couldnt_read_data"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
return;
}
loadtime = -System.currentTimeMillis();
AlignmentI al = null;
- if (format == FileFormat.Jalview)
+ if (FileFormat.Bam.equals(format))
+ {
+ FormatAdapter fa = new FormatAdapter();
+ if (source == null)
+ {
+ fa.prepareFileReader(file, protocol, format);
+ source = fa.getAlignFile();
+ }
+ if (!((BamFile) source).parseSuffix())
+ {
+ // configure a window
+ BamFileOptionsChooser bamoptions = new BamFileOptionsChooser(
+ source);
+ // ask the user which bit of the bam they want to load
+ int confirm = JvOptionPane.showConfirmDialog(null, bamoptions,
+ MessageManager.getString("label.bam_file_options"),
+ JvOptionPane.OK_CANCEL_OPTION,
+ JvOptionPane.PLAIN_MESSAGE);
+
+ if (confirm == JvOptionPane.CANCEL_OPTION
+ || confirm == JvOptionPane.CLOSED_OPTION)
+ {
+ Desktop.instance.stopLoading();
+ return;
+ }
+ else
+ {
+ bamoptions.update(source);
+ if (file.indexOf("#") == -1)
+ {
+ file = file + "#" + ((BamFile) source).suffix;
+ }
+ }
+ }
+ al = fa.readFile(file, protocol, format);
+ }
+
+ if (FileFormat.Jalview.equals(format))
{
if (source != null)
{
// Tell the user (developer?) that this is going to cause a problem
- System.err
- .println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
+ System.err.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);
}
else
{
- String error = AppletFormatAdapter.SUPPORTED_FORMATS;
- try
+ String error = AppletFormatAdapter.getSupportedFormats();
+ try
+ {
+ if (al == null)
{
if (source != null)
{
// 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.
+ boolean downloadStructureFile = format.isStructureFile()
+ && protocol.equals(DataSourceType.URL);
+ if (downloadStructureFile)
+ {
+ String structExt = format.getExtensions().split(",")[0];
+ String urlLeafName = file.substring(
+ file.lastIndexOf(
+ System.getProperty("file.separator")),
+ file.lastIndexOf("."));
+ String tempStructureFileStr = createNamedJvTempFile(
+ urlLeafName, structExt);
+ UrlDownloadClient.download(file, tempStructureFileStr);
+ al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+ format);
+ source = fa.getAlignFile();
+ }
+ else
+ {
+ al = fa.readFile(file, protocol, format);
+ source = fa.getAlignFile(); // keep reference for later if
+ // necessary.
+ }
}
- } catch (java.io.IOException ex)
- {
- error = ex.getMessage();
}
+ } catch (java.io.IOException ex)
+ {
+ error = ex.getMessage();
+ }
if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
{
{
// register PDB entries with desktop's structure selection
// manager
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).registerPDBEntry(pdbe);
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerPDBEntry(pdbe);
}
}
}
if (source instanceof ComplexAlignFile)
{
- ColumnSelection colSel = ((ComplexAlignFile) source)
- .getColumnSelection();
+ HiddenColumns colSel = ((ComplexAlignFile) source)
+ .getHiddenColumns();
SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
.getHiddenSequences();
String colourSchemeName = ((ComplexAlignFile) source)
alignFrame.getViewport().setFeaturesDisplayed(fd);
alignFrame.getViewport().setShowSequenceFeatures(
((ComplexAlignFile) source).isShowSeqFeatures());
- ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
- colourSchemeName, al);
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(colourSchemeName, al);
if (cs != null)
{
alignFrame.changeColour(cs);
.applyFeaturesStyle(proxyColourScheme);
}
alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file",
- new String[] { title }));
+ "label.successfully_loaded_file", new String[]
+ { title }));
if (raiseGUI)
{
try
{
- alignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
+ alignFrame.setMaximum(jalview.bin.Cache
+ .getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
Desktop.instance.stopLoading();
}
- final String errorMessage = MessageManager
- .getString("label.couldnt_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)
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ errorMessage,
+ MessageManager
.getString("label.error_loading_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
@Override
public void run()
{
- javax.swing.JOptionPane.showInternalMessageDialog(
- Desktop.desktop, MessageManager.formatMessage(
- "label.problems_opening_file",
- new String[] { file }), MessageManager
- .getString("label.file_open_error"),
- javax.swing.JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.problems_opening_file", new String[]
+ { file }),
+ MessageManager.getString("label.file_open_error"),
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
@Override
public void run()
{
- javax.swing.JOptionPane.showInternalMessageDialog(
- Desktop.desktop, MessageManager.formatMessage(
+ JvOptionPane.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);
+ { file }),
+ MessageManager.getString("label.out_of_memory"),
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
}
- /*
- * (non-Javadoc)
+ /**
+ * This method creates the file -
+ * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied
+ * file name and extension
*
- * @see java.lang.Object#finalize()
+ * @param fileName
+ * the name of the temp file to be created
+ * @param extension
+ * the extension of the temp file to be created
+ * @return
*/
- @Override
- protected void finalize() throws Throwable
+ private static String createNamedJvTempFile(String fileName,
+ String extension) throws IOException
{
- source = null;
- alignFrame = null;
- viewport = null;
- super.finalize();
+ String seprator = System.getProperty("file.separator");
+ String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview"
+ + seprator + System.currentTimeMillis();
+ File tempStructFile = new File(
+ jvTempDir + seprator + fileName + "." + extension);
+ tempStructFile.mkdirs();
+ return tempStructFile.toString();
}
}
git://source.jalview.org / jalview.git / blobdiff