/*
- * 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 jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeaturesSourceI;
+import jalview.bin.Cache;
+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.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+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 class FileLoader implements Runnable
{
String file;
- String protocol;
+ DataSourceType protocol;
- String format;
+ FileFormatI format;
- FileParse source = null; // alternative specification of where data comes
+ AlignmentFileReaderI source = null; // alternative specification of where data
+ // comes
// from
}
public void LoadFile(AlignViewport viewport, String file,
- String protocol, String format)
+ DataSourceType protocol, FileFormatI format)
{
this.viewport = viewport;
- LoadFile(file, protocol, format);
- }
-
- public void LoadFile(String file, String protocol, String format)
- {
this.file = file;
this.protocol = protocol;
this.format = format;
-
+
final Thread loader = new Thread(this);
-
+
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
loader.start();
}
/**
- * Load a (file, protocol) source of unknown type
- *
- * @param file
- * @param protocol
- */
- public void LoadFile(String file, String protocol)
- {
- LoadFile(file, protocol, null);
- }
-
- /**
* Load alignment from (file, protocol) and wait till loaded
*
* @param file
- * @param protocol
+ * @param sourceType
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol)
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType)
{
- return LoadFileWaitTillLoaded(file, protocol, null);
+ return LoadFileWaitTillLoaded(file, sourceType, null);
}
/**
* Load alignment from (file, protocol) of type format and wait till loaded
*
* @param file
- * @param protocol
+ * @param sourceType
* @param format
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
- String format)
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType, FileFormatI format)
{
this.file = file;
- this.protocol = protocol;
- this.format = format;
- return _LoadFileWaitTillLoaded();
- }
-
- /**
- * Load alignment from FileParse source of type format and wait till loaded
- *
- * @param source
- * @param format
- * @return alignFrame constructed from file contents
- */
- public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
- {
- this.source = source;
- file = source.getInFile();
- protocol = source.type;
+ this.protocol = sourceType;
this.format = format;
return _LoadFileWaitTillLoaded();
}
public void updateRecentlyOpened()
{
Vector recent = new Vector();
- if (protocol.equals(FormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
// do nothing if the file was pasted in as text... there is no filename to
// refer to it as.
return;
}
- String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
+ String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
: "RECENT_URL";
String historyItems = jalview.bin.Cache.getProperty(type);
newHistory.append(recent.elementAt(i));
}
- jalview.bin.Cache.setProperty(type, newHistory.toString());
+ Cache.setProperty(type, newHistory.toString());
- if (protocol.equals(FormatAdapter.FILE))
+ if (protocol == DataSourceType.FILE)
{
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+ Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
}
}
+ @Override
public void run()
{
- String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard"
+ final String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
try
// just in case the caller didn't identify the file for us
if (source != null)
{
- format = new IdentifyFile().Identify(source, false); // identify
- // stream and
- // rewind rather
- // than close
+ format = new IdentifyFile().identify(source, false);
+ // identify stream and rewind rather than close
}
else
{
- format = new IdentifyFile().Identify(file, protocol);
+ format = new IdentifyFile().identify(file, protocol);
}
+
+ }
+
+ if (format == null)
+ {
+ Desktop.instance.stopLoading();
+ System.err.println("The input file \"" + file
+ + "\" has null or unidentifiable data content!");
+ if (!Jalview.isHeadlessMode())
+ {
+ JvOptionPane.showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.couldnt_read_data")
+ + " in " + file + "\n"
+ + AppletFormatAdapter.getSupportedFormats(),
+ MessageManager.getString("label.couldnt_read_data"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ return;
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
// retrieved via URL)
if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
{
System.gc();
- memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
- // memory
- // before
- // load
+ // free memory before loading file
+ memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory());
}
loadtime = -System.currentTimeMillis();
AlignmentI al = null;
- if (format.equalsIgnoreCase("Jalview"))
+ if (FileFormat.Jalview.equals(format))
{
if (source != null)
{
.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
{
- String error = AppletFormatAdapter.SUPPORTED_FORMATS;
- if (FormatAdapter.isValidFormat(format))
+ String error = AppletFormatAdapter.getSupportedFormats();
+ try
{
- try
+ if (source != null)
{
- if (source != null)
- {
- // read from the provided source
- al = new FormatAdapter().readFromFile(source, format);
- }
- 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.
- }
- } catch (java.io.IOException ex)
- {
- error = ex.getMessage();
+ // read from the provided source
+ al = new FormatAdapter().readFromFile(source, format);
}
- }
- else
- {
- if (format != null && format.length() > 7)
+ else
{
- // ad hoc message in format.
- error = format + "\n" + error;
+
+ // 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.
}
+ } catch (java.io.IOException ex)
+ {
+ error = ex.getMessage();
}
- if ((al != null) && (al.getHeight() > 0))
+ if (!format.hasSequenceData())
{
- if (viewport != null)
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- // TODO: create undo object for this JAL-1101
- for (int i = 0; i < al.getHeight(); i++)
+ @Override
+ public void run()
{
- viewport.getAlignment().addSequence(al.getSequenceAt(i));
+ String msg = MessageManager.formatMessage("label.successfully_loaded_file_type", format.getName(), title);
+ msg = JvSwingUtils.wrapTooltip(true, msg);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ "", JvOptionPane.INFORMATION_MESSAGE);
}
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
- }
- else
+ });
+ }
+ else if ((al != null) && (al.getHeight() > 0)
+ && al.hasValidSequence())
+ {
+ // construct and register dataset sequences
+ for (SequenceI sq : al.getSequences())
{
- 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))
+ while (sq.getDatasetSequence() != null)
{
- alignFrame.setFileName(file, format);
+ sq = sq.getDatasetSequence();
}
- if (raiseGUI)
+ if (sq.getAllPDBEntries() != null)
{
- // 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);
+ for (PDBEntry pdbe : sq.getAllPDBEntries())
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(pdbe);
+ }
}
+ }
- try
- {
- alignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
- } catch (java.beans.PropertyVetoException ex)
+ FeatureSettingsModelI proxyColourScheme = source
+ .getFeatureColourScheme();
+ if (viewport != null)
+ {
+ if (proxyColourScheme != null)
{
+ viewport.applyFeaturesStyle(proxyColourScheme);
}
+ // append to existing alignment
+ viewport.addAlignment(al, title);
+ }
+ else
+ {
+ addAlignFrame(al, title);
}
}
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 (format.hasSequenceData() && raiseGUI
+ && Desktop.desktop != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
errorMessage, MessageManager
.getString("label.error_loading_file"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- javax.swing.JOptionPane.showInternalMessageDialog(
+ JvOptionPane.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);
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
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);
+ JvOptionPane.showInternalMessageDialog(
+ Desktop.desktop, MessageManager.formatMessage(
+ "warn.out_of_memory_loading_file", new String[]
+ { file }), MessageManager
+ .getString("label.out_of_memory"),
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
}
- /*
- * (non-Javadoc)
+ /**
+ * Helper method that adds the alignment as a new frame on the Desktop
*
- * @see java.lang.Object#finalize()
+ * @param al
+ * @param title
*/
- protected void finalize() throws Throwable
+ protected void addAlignFrame(AlignmentI al, String title)
{
- source = null;
- alignFrame = null;
- viewport = null;
- super.finalize();
+ // otherwise construct the alignFrame
+
+ if (source instanceof ComplexAlignFile)
+ {
+ ColumnSelection colSel = ((ComplexAlignFile) source)
+ .getColumnSelection();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+ .getDisplayedFeatures();
+ alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ alignFrame.getViewport().setFeaturesDisplayed(fd);
+ alignFrame.getViewport().setShowSequenceFeatures(
+ ((ComplexAlignFile) source).isShowSeqFeatures());
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ alignFrame.changeColour(cs);
+ }
+ }
+ else
+ {
+ alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (source instanceof FeaturesSourceI)
+ {
+ alignFrame.getViewport().setShowSequenceFeatures(true);
+ }
+ }
+ // add metadata and update ui
+ if (!(protocol == DataSourceType.PASTE))
+ {
+ alignFrame.setFileName(file, format);
+ }
+ FeatureSettingsModelI proxyColourScheme = source
+ .getFeatureColourScheme();
+ if (proxyColourScheme != null)
+ {
+ alignFrame.getViewport()
+ .applyFeaturesStyle(proxyColourScheme);
+ }
+ 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);
+ }
+
+ try
+ {
+ alignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff