*/
package jalview.gui;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Deque;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.commands.RemoveGapsCommand;
import jalview.commands.SlideSequencesCommand;
import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.AlignExportSettingsAdapter;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.HiddenSequences;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SeqCigar;
import jalview.datamodel.Sequence;
import jalview.io.TCoffeeScoreFile;
import jalview.io.vcf.VCFLoader;
import jalview.jbgui.GAlignFrame;
+import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.ServiceChangeListener;
+import jalview.ws.WSDiscovererI;
import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.PreferredServiceRegistry;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.ParamDatastoreI;
import jalview.ws.params.WsParamSetI;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.slivkaws.SlivkaWSDiscoverer;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.io.FileWriter;
import java.io.IOException;
-import java.io.PrintWriter;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
import java.util.HashSet;
-import java.util.List;
import java.util.Set;
-import java.util.Vector;
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
import javax.swing.JFileChooser;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
import javax.swing.JOptionPane;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
+@SuppressWarnings("serial")
+public class AlignFrame extends GAlignFrame
+ implements DropTargetListener, IProgressIndicator,
+ AlignViewControllerGuiI, ColourChangeListener, ServiceChangeListener
{
public static final int DEFAULT_WIDTH = 700;
*/
String fileName = null;
+ /**
+ * TODO: remove reference to 'FileObject' in AlignFrame - not correct mapping
+ */
+ File fileObject;
/**
* Creates a new AlignFrame object with specific width and height.
*/
void init()
{
+ // setBackground(Color.white); // BH 2019
+
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
if (Desktop.desktop != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- addServiceListeners();
+ if (!Platform.isJS())
+ {
+ addServiceListeners();
+ }
setGUINucleotide();
}
}
/**
+ * JavaScript will have this, maybe others. More dependable than a file name
+ * and maintains a reference to the actual bytes loaded.
+ *
+ * @param file
+ */
+ public void setFileObject(File file)
+ {
+ this.fileObject = file;
+ }
+
+ /**
* Add a KeyListener with handlers for various KeyPressed and KeyReleased
* events
*/
case KeyEvent.VK_BACK_SPACE:
if (!viewport.cursorMode)
{
- cut_actionPerformed(null);
+ cut_actionPerformed();
}
else
{
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.keyboard_editing_mode", new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
return viewport;
}
+ @Override
+ public void servicesChanged(WSDiscovererI discoverer,
+ Collection<? extends ServiceWithParameters> services)
+ {
+ buildWebServicesMenu();
+ }
+
/* Set up intrinsic listeners for dynamically generated GUI bits. */
private void addServiceListeners()
{
- final java.beans.PropertyChangeListener thisListener;
- Desktop.instance.addJalviewPropertyChangeListener("services",
- thisListener = new java.beans.PropertyChangeListener()
- {
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- // // System.out.println("Discoverer property change.");
- // if (evt.getPropertyName().equals("services"))
- {
- SwingUtilities.invokeLater(new Runnable()
- {
-
- @Override
- public void run()
- {
- System.err.println(
- "Rebuild WS Menu for service change");
- BuildWebServiceMenu();
- }
-
- });
- }
- }
- });
- addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- @Override
- public void internalFrameClosed(
- javax.swing.event.InternalFrameEvent evt)
- {
- // System.out.println("deregistering discoverer listener");
- Desktop.instance.removeJalviewPropertyChangeListener("services",
- thisListener);
- closeMenuItem_actionPerformed(true);
- };
- });
- // Finally, build the menu once to get current service state
- new Thread(new Runnable()
+ WSDiscovererI discoverer = SlivkaWSDiscoverer.getInstance();
+ discoverer.addServiceChangeListener(this);
+ }
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
+ WSDiscovererI discoverer = Jws2Discoverer.getDiscoverer();
+ discoverer.addServiceChangeListener(this);
+ }
+ // legacy event listener for compatibility with jws1
+ PropertyChangeListener legacyListener = (changeEvent) -> {
+ buildWebServicesMenu();
+ };
+ Desktop.instance.addJalviewPropertyChangeListener("services",legacyListener);
+
+ addInternalFrameListener(new InternalFrameAdapter() {
@Override
- public void run()
- {
- BuildWebServiceMenu();
+ public void internalFrameClosed(InternalFrameEvent e) {
+ System.out.println("deregistering discoverer listener");
+ SlivkaWSDiscoverer.getInstance().removeServiceChangeListener(AlignFrame.this);
+ Jws2Discoverer.getDiscoverer().removeServiceChangeListener(AlignFrame.this);
+ Desktop.instance.removeJalviewPropertyChangeListener("services", legacyListener);
+ closeMenuItem_actionPerformed(true);
}
- }).start();
+ });
+ buildWebServicesMenu();
}
/**
{
progressBar.setProgressBar(message, id);
}
+
+ @Override
+ public void removeProgressBar(long id)
+ {
+ progressBar.removeProgressBar(id);
+ }
@Override
public void registerHandler(final long id,
}
@Override
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
- new jalview.gui.SequenceFetcher(this);
+ new SequenceFetcher(this);
}
@Override
new Thread(new HMMSearch(this, args)).start();
alignPanel.repaint();
}
-
+
@Override
public void jackhmmer_actionPerformed(boolean withDefaults)
{
-
+
/*
* get default parameters, and (if requested) show
* dialog to allow modification
*/
-
+
ParamDatastoreI store = HMMERParamStore.forJackhmmer(viewport);
List<ArgumentI> args = store.getServiceParameters();
}
new Thread(new JackHMMER(this, args)).start();
alignPanel.repaint();
-
+
}
/**
}
return true;
}
-
+
@Override
protected void filterByEValue_actionPerformed()
{
viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
}
-
+
@Override
protected void filterByScore_actionPerformed()
{
viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
}
-
+
private double inputDouble(String message)
{
String str = null;
Double d = null;
- while(d == null || d <= 0)
+ while (d == null || d <= 0)
{
str = JOptionPane.showInputDialog(this.alignPanel, message);
try
{
d = Double.valueOf(str);
- }
- catch (NumberFormatException e)
+ } catch (NumberFormatException e)
{
}
}
*/
public boolean alignmentIsSufficient(int required)
{
- if (getViewport().getSequenceSelection().length < required)
- {
- JOptionPane.showMessageDialog(this,
- MessageManager.getString("label.not_enough_sequences"));
- return false;
- }
- return true;
+ if (getViewport().getSequenceSelection().length < required)
+ {
+ JOptionPane.showMessageDialog(this,
+ MessageManager.getString("label.not_enough_sequences"));
+ return false;
+ }
+ return true;
}
/**
Rectangle bounds = this.getBounds();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE;
- AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName,
- protocol, currentFileFormat);
+
+ AlignFrame newframe = null;
+
+ if (fileObject == null)
+ {
+
+ DataSourceType protocol = (fileName.startsWith("http:")
+ ? DataSourceType.URL
+ : DataSourceType.FILE);
+ newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
+ currentFileFormat);
+ }
+ else
+ {
+ newframe = loader.LoadFileWaitTillLoaded(fileObject,
+ DataSourceType.FILE, currentFileFormat);
+ }
newframe.setBounds(bounds);
if (featureSettings != null && featureSettings.isShowing())
if (fileName == null || (currentFileFormat == null)
|| fileName.startsWith("http"))
{
- saveAs_actionPerformed(null);
+ saveAs_actionPerformed();
}
else
{
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Saves the alignment to a file with a name chosen by the user, if necessary
+ * warning if a file would be overwritten
*/
@Override
- public void saveAs_actionPerformed(ActionEvent e)
+ public void saveAs_actionPerformed()
{
String format = currentFileFormat == null ? null
: currentFileFormat.getName();
int value = chooser.showSaveDialog(this);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
+ return;
+ }
+ currentFileFormat = chooser.getSelectedFormat();
+ // todo is this (2005) test now obsolete - value is never null?
+ while (currentFileFormat == null)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager
+ .getString("label.select_file_format_before_saving"),
+ MessageManager.getString("label.file_format_not_specified"),
+ JvOptionPane.WARNING_MESSAGE);
currentFileFormat = chooser.getSelectedFormat();
- while (currentFileFormat == null)
+ value = chooser.showSaveDialog(this);
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString(
- "label.select_file_format_before_saving"),
- MessageManager.getString("label.file_format_not_specified"),
- JvOptionPane.WARNING_MESSAGE);
- currentFileFormat = chooser.getSelectedFormat();
- value = chooser.showSaveDialog(this);
- if (value != JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
+ return;
}
+ }
+
+ fileName = chooser.getSelectedFile().getPath();
- fileName = chooser.getSelectedFile().getPath();
+ Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ Cache.setProperty("LAST_DIRECTORY", fileName);
+ saveAlignment(fileName, currentFileFormat);
+ }
- Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ boolean lastSaveSuccessful = false;
- Cache.setProperty("LAST_DIRECTORY", fileName);
- saveAlignment(fileName, currentFileFormat);
+ FileFormatI lastFormatSaved;
+
+ String lastFilenameSaved;
+
+ /**
+ * Raise a dialog or status message for the last call to saveAlignment.
+ *
+ * @return true if last call to saveAlignment(file, format) was successful.
+ */
+ public boolean isSaveAlignmentSuccessful()
+ {
+
+ if (!lastSaveSuccessful)
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }),
+ MessageManager.getString("label.error_saving_file"),
+ JvOptionPane.WARNING_MESSAGE);
}
+ else
+ {
+
+ setStatus(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { lastFilenameSaved, lastFormatSaved }));
+
+ }
+ return lastSaveSuccessful;
}
- public boolean saveAlignment(String file, FileFormatI format)
+ /**
+ * Saves the alignment to the specified file path, in the specified format,
+ * which may be an alignment format, or Jalview project format. If the
+ * alignment has hidden regions, or the format is one capable of including
+ * non-sequence data (features, annotations, groups), then the user may be
+ * prompted to specify what to include in the output.
+ *
+ * @param file
+ * @param format
+ */
+ public void saveAlignment(String file, FileFormatI format)
{
- boolean success = true;
+ lastSaveSuccessful = true;
+ lastFilenameSaved = file;
+ lastFormatSaved = format;
if (FileFormat.Jalview.equals(format))
{
String shortName = title;
-
- if (shortName.indexOf(java.io.File.separatorChar) > -1)
+ if (shortName.indexOf(File.separatorChar) > -1)
{
- shortName = shortName.substring(
- shortName.lastIndexOf(java.io.File.separatorChar) + 1);
+ shortName = shortName
+ .substring(shortName.lastIndexOf(File.separatorChar) + 1);
}
-
- success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+ lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
shortName);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ fileName, format }));
+ return;
}
- else
+
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable cancelAction = new Runnable()
{
- AlignmentExportData exportData = getAlignmentForExport(format,
- viewport, null);
- if (exportData.getSettings().isCancelled())
- {
- return false;
- }
- FormatAdapter f = new FormatAdapter(alignPanel,
- exportData.getSettings());
- String output = f.formatSequences(format, exportData.getAlignment(), // class
- // cast
- // exceptions
- // will
- // occur in the distant future
- exportData.getOmitHidden(), exportData.getStartEndPostions(),
- f.getCacheSuffixDefault(format),
- viewport.getAlignment().getHiddenColumns());
-
- if (output == null)
+ @Override
+ public void run()
{
- success = false;
+ lastSaveSuccessful = false;
}
- else
+ };
+ Runnable outputAction = new Runnable()
+ {
+ @Override
+ public void run()
{
- // create backupfiles object and get new temp filename destination
- BackupFiles backupfiles = new BackupFiles(file);
-
- try
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport
+ .getAlignExportData(options);
+ String output = new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns());
+ if (output == null)
{
- PrintWriter out = new PrintWriter(
- new FileWriter(backupfiles.getTempFilePath()));
-
- out.print(output);
- out.close();
- this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format.getName() }));
- } catch (Exception ex)
- {
- success = false;
- ex.printStackTrace();
+ lastSaveSuccessful = false;
}
+ else
+ {
+ // create backupfiles object and get new temp filename destination
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
+ try
+ {
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath()
+ : file;
+ PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
- backupfiles.setWriteSuccess(success);
- // do the backup file roll and rename the temp file to actual file
- success = backupfiles.rollBackupsAndRenameTempFile();
+ out.print(output);
+ out.close();
+ AlignFrame.this.setTitle(file);
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format.getName() }));
+ lastSaveSuccessful = true;
+ } catch (Exception ex)
+ {
+ lastSaveSuccessful = false;
+ ex.printStackTrace();
+ }
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ // do the backup file roll and rename the temp file to actual file
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ }
+ }
}
- }
+ };
- if (!success)
- {
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { fileName }),
- MessageManager.getString("label.error_saving_file"),
- JvOptionPane.WARNING_MESSAGE);
- }
-
- return success;
- }
-
- private void warningMessage(String warning, String title)
- {
- if (new jalview.util.Platform().isHeadless())
+ /*
+ * show dialog with export options if applicable; else just do it
+ */
+ if (AlignExportOptions.isNeeded(viewport, format))
{
- System.err.println("Warning: " + title + "\nWarning: " + warning);
-
+ AlignExportOptions choices = new AlignExportOptions(
+ alignPanel.getAlignViewport(), format, options);
+ choices.setResponseAction(0, outputAction);
+ choices.setResponseAction(1, cancelAction);
+ choices.showDialog();
}
else
{
- JvOptionPane.showInternalMessageDialog(this, warning, title,
- JvOptionPane.WARNING_MESSAGE);
+ outputAction.run();
}
- return;
}
/**
- * DOCUMENT ME!
+ * Outputs the alignment to textbox in the requested format, if necessary
+ * first prompting the user for whether to include hidden regions or
+ * non-sequence data
*
- * @param e
- * DOCUMENT ME!
+ * @param fileFormatName
*/
@Override
- protected void outputText_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(String fileFormatName)
{
FileFormatI fileFormat = FileFormats.getInstance()
- .forName(e.getActionCommand());
- AlignmentExportData exportData = getAlignmentForExport(fileFormat,
- viewport, null);
- if (exportData.getSettings().isCancelled())
- {
- return;
- }
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(null);
- try
+ .forName(fileFormatName);
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable outputAction = new Runnable()
{
- FileFormatI format = fileFormat;
- cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
- .formatSequences(format, exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getAlignment().getHiddenColumns()));
- Desktop.addInternalFrame(cap, MessageManager
- .formatMessage("label.alignment_output_command", new Object[]
- { e.getActionCommand() }), 600, 500);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Outputting alignment as " + e.getActionCommand(),
- oom);
- cap.dispose();
- }
-
- }
-
- public static AlignmentExportData getAlignmentForExport(
- FileFormatI format, AlignViewportI viewport,
- AlignExportSettingI exportSettings)
- {
- AlignmentI alignmentToExport = null;
- AlignExportSettingI settings = exportSettings;
- String[] omitHidden = null;
-
- HiddenSequences hiddenSeqs = viewport.getAlignment()
- .getHiddenSequences();
-
- alignmentToExport = viewport.getAlignment();
-
- boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
- if (settings == null)
- {
- settings = new AlignExportSettings(hasHiddenSeqs,
- viewport.hasHiddenColumns(), format);
- }
- // settings.isExportAnnotations();
-
- if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
- {
- omitHidden = viewport.getViewAsString(false,
- settings.isExportHiddenSequences());
- }
+ @Override
+ public void run()
+ {
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport
+ .getAlignExportData(options);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ try
+ {
+ FileFormatI format = fileFormat;
+ cap.setText(new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { fileFormat.getName() }), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + fileFormat.getName(),
+ oom);
+ cap.dispose();
+ }
+ }
+ };
- int[] alignmentStartEnd = new int[2];
- if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ /*
+ * show dialog with export options if applicable; else just do it
+ */
+ if (AlignExportOptions.isNeeded(viewport, fileFormat))
{
- alignmentToExport = hiddenSeqs.getFullAlignment();
+ AlignExportOptions choices = new AlignExportOptions(
+ alignPanel.getAlignViewport(), fileFormat, options);
+ choices.setResponseAction(0, outputAction);
+ choices.showDialog();
}
else
{
- alignmentToExport = viewport.getAlignment();
+ outputAction.run();
}
- alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
- .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
- AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
- omitHidden, alignmentStartEnd, settings);
- return ed;
}
/**
}
/**
- * DOCUMENT ME!
+ * Creates a PNG image of the alignment and writes it to the given file. If
+ * the file is null, the user is prompted to choose a file.
*
- * @param e
- * DOCUMENT ME!
+ * @param f
*/
@Override
public void createPNG(File f)
{
- alignPanel.makePNG(f);
+ alignPanel.makeAlignmentImage(TYPE.PNG, f);
}
/**
- * DOCUMENT ME!
+ * Creates an EPS image of the alignment and writes it to the given file. If
+ * the file is null, the user is prompted to choose a file.
*
- * @param e
- * DOCUMENT ME!
+ * @param f
*/
@Override
public void createEPS(File f)
{
- alignPanel.makeEPS(f);
+ alignPanel.makeAlignmentImage(TYPE.EPS, f);
}
+ /**
+ * Creates an SVG image of the alignment and writes it to the given file. If
+ * the file is null, the user is prompted to choose a file.
+ *
+ * @param f
+ */
@Override
public void createSVG(File f)
{
- alignPanel.makeSVG(f);
+ alignPanel.makeAlignmentImage(TYPE.SVG, f);
}
@Override
public void associatedData_actionPerformed(ActionEvent e)
throws IOException, InterruptedException
{
- // Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(
+ final JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(
- MessageManager.getString("label.load_jalview_annotations"));
- chooser.setToolTipText(
- MessageManager.getString("label.load_jalview_annotations"));
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ String tooltip = MessageManager
+ .getString("label.load_jalview_annotations");
+ chooser.setDialogTitle(tooltip);
+ chooser.setToolTipText(tooltip);
+ chooser.setResponseHandler(0, new Runnable()
{
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice, null, null, null);
- }
+ @Override
+ public void run()
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
+ }
+ });
+ chooser.showOpenDialog(this);
}
/**
* DOCUMENT ME!
*/
@Override
- protected void copy_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
{
Desktop.jalviewClipboard = new Object[] { seqs,
viewport.getAlignment().getDataset(), hiddenColumns };
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.copied_sequences_to_clipboard", new Object[]
{ Integer.valueOf(seqs.length).toString() }));
}
&& Desktop.jalviewClipboard[1] != alignment.getDataset();
// importDs==true instructs us to copy over new dataset sequences from
// an existing alignment
- Vector newDs = (importDs) ? new Vector() : null; // used to create
+ Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
+ // create
// minimum dataset set
for (int i = 0; i < sequences.length; i++)
{
// propagate alignment changed.
- viewport.getRanges().setEndSeq(alignment.getHeight());
+ viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action Cut (delete and copy) the selected region
*/
@Override
- protected void cut_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed()
{
- copy_actionPerformed(null);
- delete_actionPerformed(null);
+ copy_actionPerformed();
+ delete_actionPerformed();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Performs menu option to Delete the currently selected region
*/
@Override
- protected void delete_actionPerformed(ActionEvent evt)
+ protected void delete_actionPerformed()
{
SequenceGroup sg = viewport.getSelectionGroup();
return;
}
- /*
- * If the cut affects all sequences, warn, remove highlighted columns
- */
- if (sg.getSize() == viewport.getAlignment().getHeight())
+ Runnable okAction = new Runnable()
{
- boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
- + 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (isEntireAlignWidth)
+ @Override
+ public void run()
{
- int confirm = JvOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JvOptionPane.OK_CANCEL_OPTION);
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
+
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(),
+ sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
- if (confirm == JvOptionPane.CANCEL_OPTION
- || confirm == JvOptionPane.CLOSED_OPTION)
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
{
- return;
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
}
}
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
-
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
+ };
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
+ /*
+ * If the cut affects all sequences, prompt for confirmation
+ */
+ boolean wholeHeight = sg.getSize() == viewport.getAlignment()
+ .getHeight();
+ boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
+ + 1) == viewport.getAlignment().getWidth()) ? true : false;
+ if (wholeHeight && wholeWidth)
+ {
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+ Object[] options = new Object[] {
+ MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ dialog.showDialog(MessageManager.getString("warn.delete_all"),
+ MessageManager.getString("label.delete_all"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ }
+ else
{
- try
- {
- this.setClosed(true);
- } catch (Exception ex)
- {
- }
+ okAction.run();
}
}
column, viewport.getAlignment());
}
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_columns", new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager
+ setStatus(MessageManager
.formatMessage("label.removed_empty_columns", new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
@Override
public void alignmentProperties()
{
- JEditorPane editPane = new JEditorPane("text/html", "");
- editPane.setEditable(false);
+ JComponent pane;
StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
+
.formatAsHtml();
- editPane.setText(
- MessageManager.formatMessage("label.html_content", new Object[]
- { contents.toString() }));
+ String content = MessageManager.formatMessage("label.html_content",
+ new Object[]
+ { contents.toString() });
+ contents = null;
+
+ if (Platform.isJS())
+ {
+ JLabel textLabel = new JLabel();
+ textLabel.setText(content);
+ textLabel.setBackground(Color.WHITE);
+
+ pane = new JPanel(new BorderLayout());
+ ((JPanel) pane).setOpaque(true);
+ pane.setBackground(Color.WHITE);
+ ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ JEditorPane editPane = new JEditorPane("text/html", "");
+ editPane.setEditable(false);
+ editPane.setText(content);
+ pane = editPane;
+ }
+
JInternalFrame frame = new JInternalFrame();
- frame.getContentPane().add(new JScrollPane(editPane));
+
+ frame.getContentPane().add(new JScrollPane(pane));
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.alignment_properties", new Object[]
{
overview.dispose();
alignPanel.setOverviewPanel(null);
- };
+ }
});
if (getKeyListeners().length > 0)
{
* otherwise set the chosen colour scheme (or null for 'None')
*/
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
- viewport,
- viewport.getAlignment(), viewport.getHiddenRepSequences());
+ viewport, viewport.getAlignment(),
+ viewport.getHiddenRepSequences());
changeColour(cs);
}
alignPanel.paintAlignment(true, false);
}
-
+
/**
* DOCUMENT ME!
*
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- String filePath = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", filePath);
- NewickFile fin = null;
- try
- {
- fin = new NewickFile(filePath, DataSourceType.FILE);
- viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
- } catch (Exception ex)
- {
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager.getString("label.problem_reading_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- ex.printStackTrace();
- }
- if (fin != null && fin.hasWarningMessage())
+ @Override
+ public void run()
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- MessageManager
- .getString("label.possible_problem_with_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
+ String filePath = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", filePath);
+ NewickFile fin = null;
+ try
+ {
+ fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
+ DataSourceType.FILE));
+ viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
+ } catch (Exception ex)
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ MessageManager
+ .getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(),
+ MessageManager.getString(
+ "label.possible_problem_with_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
- }
+ });
+ chooser.showOpenDialog(this);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
return tp;
}
- private boolean buildingMenu = false;
-
/**
- * Generates menu items and listener event actions for web service clients
- *
+ * Schedule the web services menu rebuild to the event dispatch thread.
*/
- public void BuildWebServiceMenu()
+ public void buildWebServicesMenu()
{
- while (buildingMenu)
- {
- try
+ SwingUtilities.invokeLater(() -> {
+ Cache.log.info("Rebuiling WS menu");
+ webService.removeAll();
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- System.err.println("Waiting for building menu to finish.");
- Thread.sleep(10);
- } catch (Exception e)
+ SlivkaWSDiscoverer discoverer = SlivkaWSDiscoverer.getInstance();
+ JMenu submenu = new JMenu("Slivka");
+ buildWebServicesMenu(discoverer, submenu);
+ webService.add(submenu);
+ }
+ if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
+ WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer();
+ JMenu submenu = new JMenu("JABAWS");
+ buildLegacyWebServicesMenu(submenu);
+ buildWebServicesMenu(jws2servs, submenu);
+ webService.add(submenu);
}
- }
- final AlignFrame me = this;
- buildingMenu = true;
- new Thread(new Runnable()
+ });
+ }
+
+ private void buildLegacyWebServicesMenu(JMenu menu)
+ {
+ JMenu secstrmenu = new JMenu("Secondary Structure Prediction");
+ if (Discoverer.services != null && Discoverer.services.size() > 0)
{
- @Override
- public void run()
+ var secstrpred = Discoverer.services.get("SecStrPred");
+ if (secstrpred != null)
{
- final List<JMenuItem> legacyItems = new ArrayList<>();
- try
- {
- // System.err.println("Building ws menu again "
- // + Thread.currentThread());
- // TODO: add support for context dependent disabling of services based
- // on
- // alignment and current selection
- // TODO: add additional serviceHandle parameter to specify abstract
- // handler
- // class independently of AbstractName
- // TODO: add in rediscovery GUI function to restart discoverer
- // TODO: group services by location as well as function and/or
- // introduce
- // object broker mechanism.
- final Vector<JMenu> wsmenu = new Vector<>();
- final IProgressIndicator af = me;
-
- /*
- * do not i18n these strings - they are hard-coded in class
- * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
- * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
- */
- final JMenu msawsmenu = new JMenu("Alignment");
- final JMenu secstrmenu = new JMenu(
- "Secondary Structure Prediction");
- final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
- final JMenu analymenu = new JMenu("Analysis");
- final JMenu dismenu = new JMenu("Protein Disorder");
- // JAL-940 - only show secondary structure prediction services from
- // the legacy server
- if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
- // &&
- Discoverer.services != null && (Discoverer.services.size() > 0))
- {
- // TODO: refactor to allow list of AbstractName/Handler bindings to
- // be
- // stored or retrieved from elsewhere
- // No MSAWS used any more:
- // Vector msaws = null; // (Vector)
- // Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
- .get("SecStrPred");
- if (secstrpr != null)
- {
- // Add any secondary structure prediction services
- for (int i = 0, j = secstrpr.size(); i < j; i++)
- {
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
- .get(i);
- jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
- .getServiceClient(sh);
- int p = secstrmenu.getItemCount();
- impl.attachWSMenuEntry(secstrmenu, me);
- int q = secstrmenu.getItemCount();
- for (int litm = p; litm < q; litm++)
- {
- legacyItems.add(secstrmenu.getItem(litm));
- }
- }
- }
- }
-
- // Add all submenus in the order they should appear on the web
- // services menu
- wsmenu.add(msawsmenu);
- wsmenu.add(secstrmenu);
- wsmenu.add(dismenu);
- wsmenu.add(analymenu);
- // No search services yet
- // wsmenu.add(seqsrchmenu);
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- try
- {
- webService.removeAll();
- // first, add discovered services onto the webservices menu
- if (wsmenu.size() > 0)
- {
- for (int i = 0, j = wsmenu.size(); i < j; i++)
- {
- webService.add(wsmenu.get(i));
- }
- }
- else
- {
- webService.add(me.webServiceNoServices);
- }
- // TODO: move into separate menu builder class.
- boolean new_sspred = false;
- if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
- {
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
- if (jws2servs != null)
- {
- if (jws2servs.hasServices())
- {
- jws2servs.attachWSMenuEntry(webService, me);
- for (ServiceWithParameters sv : jws2servs.getServices())
- {
- if (sv.getName().toLowerCase().contains("jpred"))
- {
- for (JMenuItem jmi : legacyItems)
- {
- jmi.setVisible(false);
- }
- }
- }
-
- }
- if (jws2servs.isRunning())
- {
- JMenuItem tm = new JMenuItem(
- "Still discovering JABA Services");
- tm.setEnabled(false);
- webService.add(tm);
- }
- }
- }
- build_urlServiceMenu(me.webService);
-
-
- // TODO Mateusz - follow pattern for adding web service
- // JMenuItems for slivka-based services
-
- SlivkaWSDiscoverer slivkaDiscoverer = SlivkaWSDiscoverer.getInstance();
- if (slivkaDiscoverer.hasServices())
- {
- slivkaDiscoverer.attachWSMenuEntry(webService, me);
- } else {
- if (slivkaDiscoverer.isRunning())
- {
- {
- JMenuItem tm = new JMenuItem(
- "Still discovering Slivka Services");
- tm.setEnabled(false);
- webService.add(tm);
- }
-
- }
- }
-
-
- build_fetchdbmenu(webService);
- for (JMenu item : wsmenu)
- {
- if (item.getItemCount() == 0)
- {
- item.setEnabled(false);
- }
- else
- {
- item.setEnabled(true);
- }
- }
- } catch (Exception e)
- {
- Cache.log.debug(
- "Exception during web service menu building process.",
- e);
- }
- }
- });
- } catch (Exception e)
+ for (ext.vamsas.ServiceHandle sh : secstrpred)
{
+ var menuProvider = Discoverer.getServiceClient(sh);
+ menuProvider.attachWSMenuEntry(secstrmenu, this);
}
- buildingMenu = false;
}
- }).start();
+ }
+ menu.add(secstrmenu);
+ }
+ /**
+ * Constructs the web services menu for the given discoverer under the
+ * specified menu. This method must be called on the EDT
+ *
+ * @param discoverer
+ * the discoverer used to build the menu
+ * @param menu
+ * parent component which the elements will be attached to
+ */
+ private void buildWebServicesMenu(WSDiscovererI discoverer, JMenu menu)
+ {
+ if (discoverer.hasServices())
+ {
+ PreferredServiceRegistry.getRegistry().populateWSMenuEntry(
+ discoverer.getServices(), sv -> buildWebServicesMenu(), menu,
+ this, null);
+ }
+ if (discoverer.isRunning())
+ {
+ JMenuItem item = new JMenuItem("Service discovery in progress.");
+ item.setEnabled(false);
+ menu.add(item);
+ }
+ else if (!discoverer.hasServices())
+ {
+ JMenuItem item = new JMenuItem("No services available.");
+ item.setEnabled(false);
+ menu.add(item);
+ }
}
/**
*
* @param webService
*/
- private void build_urlServiceMenu(JMenu webService)
+ protected void build_urlServiceMenu(JMenu webService)
{
// TODO: remove this code when 2.7 is released
// DEBUG - alignmentView
* Try to load a features file onto the alignment.
*
* @param file
- * contents or path to retrieve file
+ * contents or path to retrieve file or a File object
* @param sourceType
* access mode of file (see jalview.io.AlignFile)
* @return true if features file was parsed correctly.
*/
- public boolean parseFeaturesFile(String file, DataSourceType sourceType)
+ public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
{
+ // BH 2018
return avc.parseFeaturesFile(file, sourceType,
Cache.getDefault("RELAXEDSEQIDMATCHING", false));
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
+
final AlignFrame thisaf = this;
- final List<String> files = new ArrayList<>();
+ final List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
* Object[] { String,SequenceI}
*/
ArrayList<Object[]> filesmatched = new ArrayList<>();
- ArrayList<String> filesnotmatched = new ArrayList<>();
+ ArrayList<Object> filesnotmatched = new ArrayList<>();
for (int i = 0; i < files.size(); i++)
{
- String file = files.get(i).toString();
+ // BH 2018
+ Object file = files.get(i);
+ String fileName = file.toString();
String pdbfn = "";
- DataSourceType protocol = FormatAdapter.checkProtocol(file);
+ DataSourceType protocol = (file instanceof File
+ ? DataSourceType.FILE
+ : FormatAdapter.checkProtocol(fileName));
if (protocol == DataSourceType.FILE)
{
- File fl = new File(file);
+ File fl;
+ if (file instanceof File)
+ {
+ fl = (File) file;
+ Platform.cacheFileData(fl);
+ }
+ else
+ {
+ fl = new File(fileName);
+ }
pdbfn = fl.getName();
}
else if (protocol == DataSourceType.URL)
{
- URL url = new URL(file);
+ URL url = new URL(fileName);
pdbfn = url.getFile();
}
if (pdbfn.length() > 0)
}
if (mtch != null)
{
- FileFormatI type = null;
+ FileFormatI type;
try
{
type = new IdentifyFile().identify(file, protocol);
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0],
+ .associatePdbWithSeq(fm[0].toString(),
(DataSourceType) fm[1], toassoc, false,
Desktop.instance);
if (pe != null)
{
System.err.println("Associated file : "
- + ((String) fm[0]) + " with "
+ + (fm[0].toString()) + " with "
+ toassoc.getDisplayId(true));
assocfiles++;
}
*/
for (Object[] o : filesmatched)
{
- filesnotmatched.add((String) o[0]);
+ filesnotmatched.add(o[0]);
}
}
}
{
return;
}
- for (String fn : filesnotmatched)
+ for (Object fn : filesnotmatched)
{
loadJalviewDataFile(fn, null, null, null);
}
* @throws InterruptedException
* @throws IOException
*/
- public void loadJalviewDataFile(String file, DataSourceType sourceType,
+ public void loadJalviewDataFile(Object file, DataSourceType sourceType,
FileFormatI format, SequenceI assocSeq)
{
+ // BH 2018 was String file
try
{
if (sourceType == null)
changeColour(
new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
- statusBar.setText(MessageManager.getString(
+ setStatus(MessageManager.getString(
"label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
new FileParse(file, sourceType));
sm.parse();
// todo: i18n this message
- statusBar.setText(MessageManager.formatMessage(
+ setStatus(MessageManager.formatMessage(
"label.successfully_loaded_matrix",
sm.getMatrixName()));
}
if (e.isPopupTrigger())
{
String msg = MessageManager.getString("label.enter_view_name");
- String reply = JvOptionPane.showInternalInputDialog(this, msg, msg,
- JvOptionPane.QUESTION_MESSAGE);
+ String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
+ String reply = JvOptionPane.showInputDialog(msg, ttl);
if (reply != null)
{
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
- };
+ }
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
});
rfetch.add(fetchr);
- final AlignFrame me = this;
new Thread(new Runnable()
{
@Override
public void run()
{
final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
- .getSequenceFetcherSingleton(me);
+ .getSequenceFetcherSingleton();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- String[] dbclasses = sf.getOrderedSupportedSources();
- // sf.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
- // jalview.util.QuickSort.sort(otherdb, otherdb);
+ String[] dbclasses = sf.getNonAlignmentSources();
List<DbSourceProxy> otherdb;
JMenu dfetch = new JMenu();
JMenu ifetch = new JMenu();
{
continue;
}
- // List<DbSourceProxy> dbs=otherdb;
- // otherdb=new ArrayList<DbSourceProxy>();
- // for (DbSourceProxy db:dbs)
- // {
- // if (!db.isA(DBRefSource.ALIGNMENTDB)
- // }
if (mname == null)
{
mname = "From " + dbclass;
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ final AlignFrame us = this;
+ chooser.setResponseHandler(0, new Runnable()
{
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, this);
- }
+ @Override
+ public void run()
+ {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, us);
+ }
+ });
+ chooser.showOpenDialog(null);
}
private Rectangle lastFeatureSettingsBounds = null;
+
@Override
public void setFeatureSettingsGeometry(Rectangle bounds)
{
git://source.jalview.org / jalview.git / blobdiff