*/
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.PropertyChangeEvent;
+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.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 ext.vamsas.ServiceHandle;
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.WSDiscovererI;
import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
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 $Revision$
*/
+@SuppressWarnings("serial")
public class AlignFrame extends GAlignFrame implements DropTargetListener,
IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
{
*/
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)
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
- };
+ }
});
// Finally, build the menu once to get current service state
new Thread(new Runnable()
}
@Override
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
- new jalview.gui.SequenceFetcher(this);
+ new SequenceFetcher(this);
}
@Override
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("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ Cache.setProperty("LAST_DIRECTORY", fileName);
+ saveAlignment(fileName, currentFileFormat);
+ }
+
+ boolean lastSaveSuccessful = false;
+
+ 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 }));
- Cache.setProperty("LAST_DIRECTORY", fileName);
- saveAlignment(fileName, currentFileFormat);
}
+ 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.lastIndexOf(File.separatorChar) + 1);
}
-
- success = new jalview.project.Jalview2XML().saveAlignment(this, file,
- shortName);
-
+ 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)
+ {
+ lastSaveSuccessful = false;
+ }
+ else
{
- PrintWriter out = new PrintWriter(
- new FileWriter(backupfiles.getTempFilePath()));
+ // 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));
- out.print(output);
- out.close();
- this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage(
+ 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() }));
- } catch (Exception ex)
- {
- success = false;
- ex.printStackTrace();
- }
-
- backupfiles.setWriteSuccess(success);
- // do the backup file roll and rename the temp file to actual file
- success = backupfiles.rollBackupsAndRenameTempFile();
+ 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();
}
}
/**
- * 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
- {
- 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)
+ .forName(fileFormatName);
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable outputAction = new Runnable()
{
- 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);
}
/**
closeView(alignPanel);
}
}
-
if (closeAllTabs)
{
+ if (featureSettings != null && featureSettings.isOpen())
+ {
+ featureSettings.close();
+ featureSettings = null;
+ }
/*
* this will raise an INTERNAL_FRAME_CLOSED event and this method will
* be called recursively, with the frame now in 'closed' state
* 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;
}
+ Runnable okAction = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ 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)
+ {
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }};
+
/*
- * If the cut affects all sequences, warn, remove highlighted columns
+ * If the cut affects all sequences, prompt for confirmation
*/
- if (sg.getSize() == viewport.getAlignment().getHeight())
- {
- boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
- + 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (isEntireAlignWidth)
- {
- 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);
-
- if (confirm == JvOptionPane.CANCEL_OPTION
- || confirm == JvOptionPane.CLOSED_OPTION)
- {
- return;
- }
- }
- 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)
- {
- try
- {
- this.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
+ 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
+ {
+ 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 featureSettings_actionPerformed(ActionEvent e)
{
+ showFeatureSettingsUI();
+ }
+
+ @Override
+ public FeatureSettingsControllerI showFeatureSettingsUI()
+ {
if (featureSettings != null)
{
- featureSettings.close();
+ featureSettings.closeOldSettings();
featureSettings = null;
}
if (!showSeqFeatures.isSelected())
showSeqFeatures_actionPerformed(null);
}
featureSettings = new FeatureSettings(this);
+ return featureSettings;
}
/**
@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)
{
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)
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
+ Vector<ServiceHandle> secstrpr = 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
+ final ext.vamsas.ServiceHandle sh = secstrpr
.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
}
// TODO: move into separate menu builder class.
boolean new_sspred = false;
+
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ WSDiscovererI jws2servs = Jws2Discoverer.getDiscoverer();
if (jws2servs != null)
{
if (jws2servs.hasServices())
}
}
}
- build_urlServiceMenu(me.webService);
-
-
- // TODO Mateusz - follow pattern for adding web service
- // JMenuItems for slivka-based services
- SlivkaWSDiscoverer slivkaDiscoverer = SlivkaWSDiscoverer.getInstance();
- if (slivkaDiscoverer.hasServices())
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
- slivkaDiscoverer.attachWSMenuEntry(webService, me);
- } else {
- if (slivkaDiscoverer.isRunning())
+ WSDiscovererI discoverer = SlivkaWSDiscoverer
+ .getInstance();
+ if (discoverer != null)
{
+ if (discoverer.hasServices())
+ {
+ discoverer.attachWSMenuEntry(webService, me);
+ }
+ if (discoverer.isRunning())
{
JMenuItem tm = new JMenuItem(
"Still discovering Slivka Services");
tm.setEnabled(false);
webService.add(tm);
}
-
}
}
-
+ build_urlServiceMenu(me.webService);
build_fetchdbmenu(webService);
for (JMenu item : wsmenu)
{
*
* @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 (parseFeaturesFile(file, sourceType))
{
- alignPanel.paintAlignment(true, true);
+ SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+ if (splitFrame != null)
+ {
+ splitFrame.repaint();
+ }
+ else
+ {
+ alignPanel.paintAlignment(true, true);
+ }
}
}
else
viewport = alignPanel.av;
avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
+ if (featureSettings != null && featureSettings.isOpen()
+ && featureSettings.fr.getViewport() != viewport)
+ {
+ if (viewport.isShowSequenceFeatures())
+ {
+ // refresh the featureSettings to reflect UI change
+ showFeatureSettingsUI();
+ }
+ else
+ {
+ // close feature settings for this view.
+ featureSettings.close();
+ }
+ }
+
}
/*
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"));
+ final AlignFrame us = this;
+ chooser.setResponseHandler(0, new Runnable()
+ {
+ @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);
- int value = chooser.showOpenDialog(null);
+ }
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, this);
- }
+ private Rectangle lastFeatureSettingsBounds = null;
+ @Override
+ public void setFeatureSettingsGeometry(Rectangle bounds)
+ {
+ lastFeatureSettingsBounds = bounds;
+ }
+ @Override
+ public Rectangle getFeatureSettingsGeometry()
+ {
+ return lastFeatureSettingsBounds;
}
}
*/
package jalview.gui;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.io.BackupFiles;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GSplitFrame;
-import jalview.jbgui.GStructureViewer;
-import jalview.project.Jalview2XML;
-import jalview.structure.StructureSelectionManager;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.util.UrlConstants;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.WSDiscovererI;
-import jalview.ws.params.ParamManager;
-import jalview.ws.utils.UrlDownloadClient;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.util.Hashtable;
import java.util.List;
import java.util.ListIterator;
-import java.util.StringTokenizer;
import java.util.Vector;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import javax.swing.JPanel;
import javax.swing.JPopupMenu;
import javax.swing.JProgressBar;
+import javax.swing.JTextField;
import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
import javax.swing.event.HyperlinkEvent;
import org.stackoverflowusers.file.WindowsShortcut;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.io.BackupFiles;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
+import jalview.project.Jalview2XML;
+import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker.TYPE;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.ShortcutKeyMaskExWrapper;
+import jalview.util.UrlConstants;
+import jalview.viewmodel.AlignmentViewport;
++import jalview.ws.WSDiscovererI;
+import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
+
/**
* Jalview Desktop
*
implements DropTargetListener, ClipboardOwner, IProgressIndicator,
jalview.api.StructureSelectionManagerProvider
{
+ private static final String CITATION = "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
+ + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+ + "<br><br>If you use Jalview, please cite:"
+ + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+ + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+ + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033";
+
+ private static final String DEFAULT_AUTHORS = "The Jalview Authors (See AUTHORS file for current list)";
+
private static int DEFAULT_MIN_WIDTH = 300;
private static int DEFAULT_MIN_HEIGHT = 250;
protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
- public static HashMap<String, FileWriter> savingFiles = new HashMap<>();
+ public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
public static MyDesktopPane desktop;
+ public static MyDesktopPane getDesktop()
+ {
+ // BH 2018 could use currentThread() here as a reference to a
+ // Hashtable<Thread, MyDesktopPane> in JavaScript
+ return desktop;
+ }
+
static int openFrameCount = 0;
static final int xOffset = 30;
*/
public Desktop()
{
+ super();
/**
* A note to implementors. It is ESSENTIAL that any activities that might
* block are spawned off as threads rather than waited for during this
instance = this;
doConfigureStructurePrefs();
- setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+ setTitle("Jalview " + Cache.getProperty("VERSION"));
/*
if (!Platform.isAMac())
{
try
{
APQHandlers.setAPQHandlers(this);
- } catch (Exception e)
- {
- System.out.println("Cannot set APQHandlers");
- // e.printStackTrace();
} catch (Throwable t)
{
- System.out.println("Cannot set APQHandlers");
+ System.out.println("Error setting APQHandlers: " + t.toString());
// t.printStackTrace();
}
-
addWindowListener(new WindowAdapter()
{
}
});
- boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
+ boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE",
false);
- boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
+ boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE",
false);
desktop = new MyDesktopPane(selmemusage);
+
showMemusage.setSelected(selmemusage);
desktop.setBackground(Color.white);
// JScrollPane sp = new JScrollPane();
// sp.getViewport().setView(desktop);
// getContentPane().add(sp, BorderLayout.CENTER);
+
+ // BH 2018 - just an experiment to try unclipped JInternalFrames.
+ if (Platform.isJS())
+ {
+ getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
+ }
+
getContentPane().add(desktop, BorderLayout.CENTER);
desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
desktop.setDesktopManager(new MyDesktopManager(
- (Platform.isWindows() ? new DefaultDesktopManager()
- : Platform.isAMac()
+ (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS()
? new AquaInternalFrameManager(
desktop.getDesktopManager())
: desktop.getDesktopManager())));
else
{
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
- 900, 650);
+ int xPos = Math.max(5, (screenSize.width - 900) / 2);
+ int yPos = Math.max(5, (screenSize.height - 650) / 2);
+ setBounds(xPos, yPos, 900, 650);
}
- jconsole = new Console(this, showjconsole);
- // add essential build information
- jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole());
- showConsole(showjconsole);
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ jconsole = new Console(this, showjconsole);
+ jconsole.setHeader(Cache.getVersionDetailsForConsole());
+ showConsole(showjconsole);
+
+ showNews.setVisible(false);
+
+ experimentalFeatures.setSelected(showExperimental());
+
+ getIdentifiersOrgData();
- showNews.setVisible(false);
+ checkURLLinks();
+
+ // Spawn a thread that shows the splashscreen
+
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ new SplashScreen(true);
+ }
+ });
- experimentalFeatures.setSelected(showExperimental());
+ // Thread off a new instance of the file chooser - this reduces the time
+ // it
+ // takes to open it later on.
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ Cache.log.debug("Filechooser init thread started.");
+ String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+ JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+ fileFormat);
+ Cache.log.debug("Filechooser init thread finished.");
+ }
+ }).start();
+ // Add the service change listener
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
+ {
- getIdentifiersOrgData();
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ Cache.log.debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
+ });
+ }
- checkURLLinks();
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
this.addWindowListener(new WindowAdapter()
{
});
desktop.addMouseListener(ma);
- this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
- // Spawn a thread that shows the splashscreen
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- new SplashScreen();
- }
- });
-
- // Thread off a new instance of the file chooser - this reduces the time it
- // takes to open it later on.
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- Cache.log.debug("Filechooser init thread started.");
- String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
- fileFormat);
- Cache.log.debug("Filechooser init thread finished.");
- }
- }).start();
- // Add the service change listener
- changeSupport.addJalviewPropertyChangeListener("services",
- new PropertyChangeListener()
- {
-
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- Cache.log.debug("Firing service changed event for "
- + evt.getNewValue());
- JalviewServicesChanged(evt);
- }
-
- });
}
/**
// configure services
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(this);
- if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
+ if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
{
- ssm.setAddTempFacAnnot(jalview.bin.Cache
+ ssm.setAddTempFacAnnot(Cache
.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(jalview.bin.Cache
+ ssm.setProcessSecondaryStructure(Cache
.getDefault(Preferences.STRUCT_FROM_PDB, true));
ssm.setSecStructServices(
- jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
+ Cache.getDefault(Preferences.USE_RNAVIEW, true));
}
else
{
public void run()
{
Cache.log.debug("Starting news thread.");
-
jvnews = new BlogReader(me);
showNews.setVisible(true);
Cache.log.debug("Completed news thread.");
public void run()
{
Cache.log.debug("Downloading data from identifiers.org");
- UrlDownloadClient client = new UrlDownloadClient();
try
{
- client.download(IdOrgSettings.getUrl(),
+ UrlDownloadClient.download(IdOrgSettings.getUrl(),
IdOrgSettings.getDownloadLocation());
} catch (IOException e)
{
}
}
}).start();
- ;
+
}
@Override
void showNews(boolean visible)
{
+ Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+ showNews.setSelected(visible);
+ if (visible && !jvnews.isVisible())
{
- Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
- showNews.setSelected(visible);
- if (visible && !jvnews.isVisible())
+ new Thread(new Runnable()
{
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
- {
- long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(
- MessageManager.getString("status.refreshing_news"),
- now);
- jvnews.refreshNews();
- Desktop.instance.setProgressBar(null, now);
- jvnews.showNews();
- }
- }).start();
- }
+ long now = System.currentTimeMillis();
+ Desktop.instance.setProgressBar(
+ MessageManager.getString("status.refreshing_news"), now);
+ jvnews.refreshNews();
+ Desktop.instance.setProgressBar(null, now);
+ jvnews.showNews();
+ }
+ }).start();
}
}
{
// TODO: lock aspect ratio for scaling desktop Bug #0058199
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
- String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
- String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
- String width = jalview.bin.Cache
+ String x = Cache.getProperty(windowName + "SCREEN_X");
+ String y = Cache.getProperty(windowName + "SCREEN_Y");
+ String width = Cache
.getProperty(windowName + "SCREEN_WIDTH");
- String height = jalview.bin.Cache
+ String height = Cache
.getProperty(windowName + "SCREEN_HEIGHT");
if ((x != null) && (y != null) && (width != null) && (height != null))
{
int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
iw = Integer.parseInt(width), ih = Integer.parseInt(height);
- if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
+ if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
{
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
- jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+ Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
- jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
+ Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
ih = (int) (ih * sh);
while (ix >= screenSize.width)
{
- jalview.bin.Cache.log.debug(
+ Cache.log.debug(
"Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
while (iy >= screenSize.height)
{
- jalview.bin.Cache.log.debug(
+ Cache.log.debug(
"Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- jalview.bin.Cache.log.debug(
+ Cache.log.debug(
"Got last known dimensions for " + windowName + ": x:" + ix
+ " y:" + iy + " width:" + iw + " height:" + ih);
}
frame.setResizable(resizable);
frame.setMaximizable(resizable);
frame.setIconifiable(resizable);
- frame.setOpaque(false);
+ frame.setOpaque(Platform.isJS());
if (frame.getX() < 1 && frame.getY() < 1)
{
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
- };
+ }
});
menuItem.addActionListener(new ActionListener()
frame.setIcon(false);
} catch (java.beans.PropertyVetoException ex)
{
-
+ // System.err.println(ex.toString());
}
}
});
}
/**
- * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
- * the window
+ * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the
+ * window
*
* @param frame
*/
KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
InputEvent.CTRL_DOWN_MASK);
KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
+ ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
InputMap inputMap = frame
.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
- List<String> files = new ArrayList<>();
+ List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
{
for (int i = 0; i < files.size(); i++)
{
- String file = files.get(i).toString();
+ // BH 2018 File or String
+ Object file = files.get(i);
+ String fileName = file.toString();
DataSourceType protocol = (protocols == null)
? DataSourceType.FILE
: protocols.get(i);
FileFormatI format = null;
- if (file.endsWith(".jar"))
+ if (fileName.endsWith(".jar"))
{
format = FileFormat.Jalview;
{
format = new IdentifyFile().identify(file, protocol);
}
-
- new FileLoader().LoadFile(file, protocol, format);
+ if (file instanceof File)
+ {
+ Platform.cacheFileData((File) file);
+ }
+ new FileLoader().LoadFile(null, file, protocol, format);
}
} catch (Exception ex)
MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ @Override
+ public void run()
+ {
+ File selectedFile = chooser.getSelectedFile();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- FileFormatI format = chooser.getSelectedFormat();
+ FileFormatI format = chooser.getSelectedFormat();
- /*
- * Call IdentifyFile to verify the file contains what its extension implies.
- * Skip this step for dynamically added file formats, because
- * IdentifyFile does not know how to recognise them.
- */
- if (FileFormats.getInstance().isIdentifiable(format))
- {
- try
- {
- format = new IdentifyFile().identify(choice, DataSourceType.FILE);
- } catch (FileFormatException e)
+ /*
+ * Call IdentifyFile to verify the file contains what its extension implies.
+ * Skip this step for dynamically added file formats, because
+ * IdentifyFile does not know how to recognise them.
+ */
+ if (FileFormats.getInstance().isIdentifiable(format))
{
- // format = null; //??
+ try
+ {
+ format = new IdentifyFile().identify(selectedFile,
+ DataSourceType.FILE);
+ } catch (FileFormatException e)
+ {
+ // format = null; //??
+ }
}
- }
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE,
- format);
+ new FileLoader().LoadFile(viewport, selectedFile,
+ DataSourceType.FILE, format);
}
- else
- {
- new FileLoader().LoadFile(choice, DataSourceType.FILE, format);
- }
- }
+ });
+ chooser.showOpenDialog(this);
}
/**
- * DOCUMENT ME!
+ * Shows a dialog for input of a URL at which to retrieve alignment data
*
- * @param e
- * DOCUMENT ME!
+ * @param viewport
*/
@Override
public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
// for viewing
JLabel label = new JLabel(
MessageManager.getString("label.input_file_url"));
JPanel panel = new JPanel(new GridLayout(2, 1));
panel.add(label);
- panel.add(history);
- history.setPreferredSize(new Dimension(400, 20));
- history.setEditable(true);
- history.addItem("http://www.");
-
- String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
-
- StringTokenizer st;
-
- if (historyItems != null)
- {
- st = new StringTokenizer(historyItems, "\t");
-
- while (st.hasMoreTokens())
- {
- history.addItem(st.nextElement());
- }
- }
- int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
- MessageManager.getString("label.input_alignment_from_url"),
- JvOptionPane.OK_CANCEL_OPTION);
-
- if (reply != JvOptionPane.OK_OPTION)
+ /*
+ * the URL to fetch is
+ * Java: an editable combobox with history
+ * JS: (pending JAL-3038) a plain text field
+ */
+ JComponent history;
+ String urlBase = "http://www.";
+ if (Platform.isJS())
{
- return;
+ history = new JTextField(urlBase, 35);
}
-
- String url = history.getSelectedItem().toString();
-
- if (url.toLowerCase().endsWith(".jar"))
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
{
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- else
+ JComboBox<String> asCombo = new JComboBox<>();
+ asCombo.setPreferredSize(new Dimension(400, 20));
+ asCombo.setEditable(true);
+ asCombo.addItem(urlBase);
+ String historyItems = Cache.getProperty("RECENT_URL");
+ if (historyItems != null)
{
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
+ for (String token : historyItems.split("\\t"))
+ {
+ asCombo.addItem(token);
+ }
}
+ history = asCombo;
}
- else
+ panel.add(history);
+
+ Object[] options = new Object[] { MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ Runnable action = new Runnable()
{
- FileFormatI format = null;
- try
- {
- format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e)
+ @Override
+ public void run()
{
- // TODO revise error handling, distinguish between
- // URL not found and response not valid
- }
+ @SuppressWarnings("unchecked")
+ String url = (history instanceof JTextField
+ ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getSelectedItem()
+ .toString());
- if (format == null)
- {
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.couldnt_locate",
- new Object[]
- { url }),
- MessageManager.getString("label.url_not_found"),
- JvOptionPane.WARNING_MESSAGE);
+ if (url.toLowerCase().endsWith(".jar"))
+ {
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ }
+ else
+ {
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(url, DataSourceType.URL);
+ } catch (FileFormatException e)
+ {
+ // TODO revise error handling, distinguish between
+ // URL not found and response not valid
+ }
- return;
- }
+ if (format == null)
+ {
+ String msg = MessageManager
+ .formatMessage("label.couldnt_locate", url);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- format);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL, format);
+ return;
+ }
+
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ format);
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, DataSourceType.URL, format);
+ }
+ }
}
- }
+ };
+ String dialogOption = MessageManager
+ .getString("label.input_alignment_from_url");
+ JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action)
+ .showInternalDialog(panel, dialogOption,
+ JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.PLAIN_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
}
/**
public void quit()
{
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
+ Cache.setProperty("SCREENGEOMETRY_WIDTH",
screen.width + "");
- jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
+ Cache.setProperty("SCREENGEOMETRY_HEIGHT",
screen.height + "");
storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
getWidth(), getHeight()));
private void storeLastKnownDimensions(String string, Rectangle jc)
{
- jalview.bin.Cache.log.debug("Storing last known dimensions for "
+ Cache.log.debug("Storing last known dimensions for "
+ string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ " height:" + jc.height);
- jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
- jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
- jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
- jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
+ Cache.setProperty(string + "SCREEN_X", jc.x + "");
+ Cache.setProperty(string + "SCREEN_Y", jc.y + "");
+ Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
+ Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
}
/**
@Override
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
- // StringBuffer message = getAboutMessage(false);
- // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- //
- // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
new Thread(new Runnable()
{
@Override
public void run()
{
- new SplashScreen(true);
+ new SplashScreen(false);
}
}).start();
}
- public StringBuffer getAboutMessage(boolean shortv)
+ /**
+ * Returns the html text for the About screen, including any available version
+ * number, build details, author details and citation reference, but without
+ * the enclosing {@code html} tags
+ *
+ * @return
+ */
+ public String getAboutMessage()
{
- StringBuffer message = new StringBuffer();
- message.append("<html>");
- if (shortv)
- {
- message.append("<h1><strong>Version: "
- + jalview.bin.Cache.getProperty("VERSION")
- + "</strong></h1>");
- message.append("<strong>Built: <em>"
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
- + "</em> from " + jalview.bin.Cache.getBuildDetailsForSplash()
- + "</strong>");
+ StringBuilder message = new StringBuilder(1024);
+ message.append("<h1><strong>Version: ")
+ .append(Cache.getProperty("VERSION")).append("</strong></h1>")
+ .append("<strong>Built: <em>")
+ .append(Cache.getDefault("BUILD_DATE", "unknown"))
+ .append("</em> from ").append(Cache.getBuildDetailsForSplash())
+ .append("</strong>");
- }
- else
- {
-
- message.append("<strong>Version "
- + jalview.bin.Cache.getProperty("VERSION")
- + "; last updated: "
- + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
- }
-
- if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
- .equals("Checking"))
+ String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
+ if (latestVersion.equals("Checking"))
{
// JBP removed this message for 2.11: May be reinstated in future version
// message.append("<br>...Checking latest version...</br>");
}
- else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
- .equals(jalview.bin.Cache.getProperty("VERSION")))
+ else if (!latestVersion.equals(Cache.getProperty("VERSION")))
{
boolean red = false;
- if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
+ if (Cache.getProperty("VERSION").toLowerCase()
.indexOf("automated build") == -1)
{
red = true;
message.append("<div style=\"color: #FF0000;font-style: bold;\">");
}
- message.append("<br>!! Version "
- + jalview.bin.Cache.getDefault("LATEST_VERSION",
- "..Checking..")
- + " is available for download from "
- + jalview.bin.Cache.getDefault("www.jalview.org",
- "http://www.jalview.org")
- + " !!");
+ message.append("<br>!! Version ")
+ .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
+ .append(" is available for download from ")
+ .append(Cache.getDefault("www.jalview.org",
+ "http://www.jalview.org"))
+ .append(" !!");
if (red)
{
message.append("</div>");
}
}
- message.append("<br>Authors: " + jalview.bin.Cache.getDefault(
- "AUTHORFNAMES",
- "The Jalview Authors (See AUTHORS file for current list)")
- + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
- + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
- + "<br><br>If you use Jalview, please cite:"
- + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
- + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
- + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
- + "</html>");
- return message;
+ message.append("<br>Authors: ");
+ message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
+ message.append(CITATION);
+
+ return message.toString();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action on requesting Help documentation
*/
@Override
- public void documentationMenuItem_actionPerformed(ActionEvent e)
+ public void documentationMenuItem_actionPerformed()
{
try
{
- Help.showHelpWindow();
+ if (Platform.isJS())
+ {
+ BrowserLauncher.openURL("http://www.jalview.org/help.html");
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ Help.showHelpWindow();
+ }
} catch (Exception ex)
{
+ System.err.println("Error opening help: " + ex.getMessage());
}
}
protected void garbageCollect_actionPerformed(ActionEvent e)
{
// We simply collect the garbage
- jalview.bin.Cache.log.debug("Collecting garbage...");
+ Cache.log.debug("Collecting garbage...");
System.gc();
- jalview.bin.Cache.log.debug("Finished garbage collection.");
+ Cache.log.debug("Finished garbage collection.");
}
/*
*/
void showConsole(boolean selected)
{
- showConsole.setSelected(selected);
// TODO: decide if we should update properties file
- Cache.setProperty("SHOW_JAVA_CONSOLE",
- Boolean.valueOf(selected).toString());
- jconsole.setVisible(selected);
+ if (jconsole != null) // BH 2018
+ {
+ showConsole.setSelected(selected);
+ Cache.setProperty("SHOW_JAVA_CONSOLE",
+ Boolean.valueOf(selected).toString());
+ jconsole.setVisible(selected);
+ }
}
void reorderAssociatedWindows(boolean minimize, boolean close)
}
/**
- * Shows a file chooser dialog and writes out the current session as a Jalview
- * project file
+ * Prompts the user to choose a file and then saves the Jalview state as a
+ * Jalview project file
*/
@Override
public void saveState_actionPerformed()
setProgressBar(MessageManager.formatMessage(
"label.saving_jalview_project", new Object[]
{ chosenFile.getName() }), chosenFile.hashCode());
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ Cache.setProperty("LAST_DIRECTORY",
chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
try
{
- BackupFiles backupfiles = new BackupFiles(chosenFile);
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
- new Jalview2XML().saveState(backupfiles.getTempFile());
+ new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
- backupfiles.setWriteSuccess(true);
- backupfiles.rollBackupsAndRenameTempFile();
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(true);
+ backupfiles.rollBackupsAndRenameTempFile();
+ }
} catch (OutOfMemoryError oom)
{
new OOMWarning("Whilst saving current state to "
setProgressBar(null, chosenFile.hashCode());
}
}).start();
- }
+ }
}
@Override
// allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ chooser.setResponseHandler(0, new Runnable()
{
- final File selectedFile = chooser.getSelectedFile();
- setProjectFile(selectedFile);
- final String choice = selectedFile.getAbsolutePath();
- Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ String choice = selectedFile.getAbsolutePath();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ new Thread(new Runnable()
{
- setProgressBar(MessageManager.formatMessage(
- "label.loading_jalview_project", new Object[]
- { choice }), choice.hashCode());
- try
- {
- new Jalview2XML().loadJalviewAlign(choice);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
+ @Override
+ public void run()
{
- Cache.log.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager.getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
+ try
+ {
+ new Jalview2XML().loadJalviewAlign(selectedFile);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ Cache.log.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager.getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
}
- setProgressBar(null, choice.hashCode());
- }
- }).start();
- }
+ }).start();
+ }
+ });
+
+ chooser.showOpenDialog(this);
}
@Override
ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
- public void startLoading(final String fileName)
+ public void startLoading(final Object fileName)
{
if (fileLoadingCount == 0)
{
return;
}
+ // FIXME: ideally should use UI interface API
+ FeatureSettings viewFeatureSettings = (af.featureSettings != null
+ && af.featureSettings.isOpen())
+ ? af.featureSettings
+ : null;
+ Rectangle fsBounds = af.getFeatureSettingsGeometry();
for (int i = 0; i < size; i++)
{
AlignmentPanel ap = af.alignPanels.get(i);
+
AlignFrame newaf = new AlignFrame(ap);
+ // transfer reference for existing feature settings to new alignFrame
+ if (ap == af.alignPanel)
+ {
+ if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+ {
+ newaf.featureSettings = viewFeatureSettings;
+ }
+ newaf.setFeatureSettingsGeometry(fsBounds);
+ }
+
/*
* Restore the view's last exploded frame geometry if known. Multiple
* views from one exploded frame share and restore the same (frame)
addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+ // and materialise a new feature settings dialog instance for the new alignframe
+ // (closes the old as if 'OK' was pressed)
+ if (ap == af.alignPanel && newaf.featureSettings != null
+ && newaf.featureSettings.isOpen()
+ && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+ {
+ newaf.showFeatureSettingsUI();
+ }
}
+ af.featureSettings = null;
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
/**
* Gather expanded views (separate AlignFrame's) with the same sequence set
- * identifier back in to this frame as additional views, and close the
- * expanded views. Note the expanded frames may themselves have multiple
- * views. We take the lot.
+ * identifier back in to this frame as additional views, and close the expanded
+ * views. Note the expanded frames may themselves have multiple views. We take
+ * the lot.
*
* @param source
*/
source.viewport.setExplodedGeometry(source.getBounds());
JInternalFrame[] frames = desktop.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
-
for (int t = 0; t < frames.length; t++)
{
if (frames[t] instanceof AlignFrame && frames[t] != source)
if (gatherThis)
{
+ if (af.featureSettings != null && af.featureSettings.isOpen())
+ {
+ if (source.featureSettings == null)
+ {
+ // preserve the feature settings geometry for this frame
+ source.featureSettings = af.featureSettings;
+ source.setFeatureSettingsGeometry(
+ af.getFeatureSettingsGeometry());
+ }
+ else
+ {
+ // close it and forget
+ af.featureSettings.close();
+ }
+ }
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
}
}
}
+ // refresh the feature setting UI for the source frame if it exists
+ if (source.featureSettings != null
+ && source.featureSettings.isOpen())
+ {
+ source.showFeatureSettingsUI();
+ }
}
public JInternalFrame[] getAllFrames()
/**
* Proxy class for JDesktopPane which optionally displays the current memory
- * usage and highlights the desktop area with a red bar if free memory runs
- * low.
+ * usage and highlights the desktop area with a red bar if free memory runs low.
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane implements Runnable
+ public class MyDesktopPane extends JDesktopPane
+ implements Runnable
{
-
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
openGroovyConsole();
} catch (Exception ex)
{
- jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+ Cache.log.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_create_groovy_shell"),
}
/**
- * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
- * binding when opened
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding
+ * when opened
*/
protected void addQuitHandler()
{
@Override
public void setProgressBar(String message, long id)
{
+ // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
+
if (progressBars == null)
{
progressBars = new Hashtable<>();
}
/**
- * This will return the first AlignFrame holding the given viewport instance.
- * It will break if there are more than one AlignFrames viewing a particular
- * av.
+ * This will return the first AlignFrame holding the given viewport instance. It
+ * will break if there are more than one AlignFrames viewing a particular av.
*
* @param viewport
* @return alignFrame for viewport
public void startServiceDiscovery(boolean blocking)
{
boolean alive = true;
- Thread t0 = null, t1 = null, t2 = null;
+ Thread t0 = null, t1 = null, t2 = null, t3 = null;
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
if (true)
{
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .startDiscoverer(changeSupport);
+ t2 = startServiceDiscovery(
+ jalview.ws.jws2.Jws2Discoverer.getDiscoverer(), false);
}
- Thread t3 = null;
+ if (Cache.getDefault("SHOW_SLIVKA_SERVICES", true))
{
// start slivka discovery
- t3 = new Thread(jalview.ws.slivkaws.SlivkaWSDiscoverer.getInstance());
- t3.start();
+ t3 = startServiceDiscovery(
+ jalview.ws.slivkaws.SlivkaWSDiscoverer.getInstance(), false);
}
if (blocking)
{
} catch (Exception e)
{
}
+ // FIXME: Condition should check the discoverer's isRunning rather than
+ // threads
alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
- || (t3 != null && t3.isAlive())
- || (t0 != null && t0.isAlive());
+ || (t3 != null && t3.isAlive()) || (t0 != null && t0.isAlive());
}
}
}
+ public Thread startServiceDiscovery(WSDiscovererI discoverer,
+ boolean blocking)
+ {
+ Thread thread = discoverer.startDiscoverer(changeSupport);
+ if (blocking)
+ {
+ try
+ {
+ thread.join();
+ } catch (InterruptedException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ return thread;
+ }
+
/**
* called to check if the service discovery process completed successfully.
*
{
if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
{
- final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
- .getErrorMessages();
+ final WSDiscovererI discoverer = jalview.ws.jws2.Jws2Discoverer
+ .getDiscoverer();
+ final String ermsg = discoverer.getErrorMessages();
if (ermsg != null)
{
if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
} catch (InterruptedException x)
{
}
- ;
}
if (instance == null)
{
block.release();
}
+ /**
+ * Outputs an image of the desktop to file in EPS format, after prompting the
+ * user for choice of Text or Lineart character rendering (unless a preference
+ * has been set). The file name is generated as
+ *
+ * <pre>
+ * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds
+ * </pre>
+ */
@Override
protected void snapShotWindow_actionPerformed(ActionEvent e)
{
+ // currently the menu option to do this is not shown
invalidate();
- File of;
- ImageMaker im = new jalview.util.ImageMaker(
- this, ImageMaker.TYPE.EPS, "View of Desktop", getWidth(),
- getHeight(), of = new File("Jalview_snapshot"
- + System.currentTimeMillis() + ".eps"),
- "View of desktop", null, 0, false);
- try
- {
- paintAll(im.getGraphics());
- im.writeImage();
- } catch (Exception q)
+
+ int width = getWidth();
+ int height = getHeight();
+ File of = new File(
+ "Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
+ ImageWriterI writer = new ImageWriterI()
{
- Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
- q);
- return;
- }
- Cache.log.info("Successfully written snapshot to file "
- + of.getAbsolutePath());
+ @Override
+ public void exportImage(Graphics g) throws Exception
+ {
+ paintAll(g);
+ Cache.log.info("Successfully written snapshot to file "
+ + of.getAbsolutePath());
+ }
+ };
+ String title = "View of desktop";
+ ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
+ title);
+ exporter.doExport(of, this, width, height, title);
}
/**
* Explode the views in the given SplitFrame into separate SplitFrame windows.
- * This respects (remembers) any previous 'exploded geometry' i.e. the size
- * and location last time the view was expanded (if any). However it does not
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size and
+ * location last time the view was expanded (if any). However it does not
* remember the split pane divider location - this is set to match the
* 'exploding' frame.
*
* - the payload from the drop event
* @throws Exception
*/
- public static void transferFromDropTarget(List<String> files,
+ public static void transferFromDropTarget(List<Object> files,
List<DataSourceType> protocols, DropTargetDropEvent evt,
Transferable t) throws Exception
{
+ // BH 2018 changed List<String> to List<Object> to allow for File from SwingJS
+
+ // DataFlavor[] flavors = t.getTransferDataFlavors();
+ // for (int i = 0; i < flavors.length; i++) {
+ // if (flavors[i].isFlavorJavaFileListType()) {
+ // evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ // List<File> list = (List<File>) t.getTransferData(flavors[i]);
+ // for (int j = 0; j < list.size(); j++) {
+ // File file = (File) list.get(j);
+ // byte[] data = getDroppedFileBytes(file);
+ // fileName.setText(file.getName() + " - " + data.length + " " +
+ // evt.getLocation());
+ // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent();
+ // target.setText(new String(data));
+ // }
+ // dtde.dropComplete(true);
+ // return;
+ // }
+ //
+
DataFlavor uriListFlavor = new DataFlavor(
"text/uri-list;class=java.lang.String"), urlFlavour = null;
try
}
else
{
- if (Platform.isAMac())
+ if (Platform.isAMacAndNotJS())
{
System.err.println(
"Please ignore plist error - occurs due to problem with java 8 on OSX");
}
- ;
}
} catch (Throwable ex)
{
for (Object file : (List) t
.getTransferData(DataFlavor.javaFileListFlavor))
{
- files.add(((File) file).toString());
+ files.add(file);
protocols.add(DataSourceType.FILE);
}
}
}
}
}
- if (Platform.isWindows())
-
+ if (Platform.isWindowsAndNotJS())
{
Cache.log.debug("Scanning dropped content for Windows Link Files");
// resolve any .lnk files in the file drop
for (int f = 0; f < files.size(); f++)
{
- String source = files.get(f).toLowerCase();
+ String source = files.get(f).toString().toLowerCase();
if (protocols.get(f).equals(DataSourceType.FILE)
&& (source.endsWith(".lnk") || source.endsWith(".url")
|| source.endsWith(".site")))
{
try
{
- File lf = new File(files.get(f));
+ Object obj = files.get(f);
+ File lf = (obj instanceof File ? (File) obj
+ : new File((String) obj));
// process link file to get a URL
Cache.log.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
}
/**
- * Answers a (possibly empty) list of any structure viewer frames (currently
- * for either Jmol or Chimera) which are currently open. This may optionally
- * be restricted to viewers of a specified class, or viewers linked to a
- * specified alignment panel.
+ * Answers a (possibly empty) list of any structure viewer frames (currently for
+ * either Jmol or Chimera) which are currently open. This may optionally be
+ * restricted to viewers of a specified class, or viewers linked to a specified
+ * alignment panel.
*
* @param apanel
* if not null, only return viewers linked to this panel
import java.util.List;
import javax.help.HelpSetException;
-import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JInternalFrame;
import javax.swing.JPanel;
private WsPreferences wsPrefs;
+ private SlivkaPreferences slivkaPrefs;
+
private OptionsParam promptEachTimeOpt = new OptionsParam(
MessageManager.getString("label.prompt_each_time"),
"Prompt each time");
super();
frame = new JInternalFrame();
frame.setContentPane(this);
- wsPrefs = new WsPreferences();
- wsTab.add(wsPrefs, BorderLayout.CENTER);
- slivkaTab.add(slivkaPrefs = new SlivkaPreferences(),
- BorderLayout.CENTER);
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ wsPrefs = new WsPreferences();
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
++ slivkaPrefs = new SlivkaPreferences();
++ slivkaTab.add(slivkaPrefs, BorderLayout.CENTER);
+ }
int width = 500, height = 450;
- new jalview.util.Platform();
- if (Platform.isAMac())
+ if (Platform.isAMacAndNotJS())
{
width = 570;
height = 480;
fontStyleCB.setSelectedItem(
Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
- smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+ smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
scaleProteinToCdna
.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
sorter.setSortKeys(sortKeys);
- sorter.sort();
+ // BH 2018 setSortKeys will do the sort
+ // sorter.sort();
// set up filtering
ActionListener onReset;
doReset.addActionListener(onReset);
// filter to display only custom urls
- final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
+ final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
{
@Override
public boolean include(
/*
* Set Output tab defaults
*/
- epsRendering.addItem(promptEachTimeOpt);
- epsRendering.addItem(lineArtOpt);
- epsRendering.addItem(textOpt);
- String defaultEPS = Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
- if (defaultEPS.equalsIgnoreCase("Text"))
- {
- epsRendering.setSelectedItem(textOpt);
- }
- else if (defaultEPS.equalsIgnoreCase("Lineart"))
- {
- epsRendering.setSelectedItem(lineArtOpt);
- }
- else
- {
- epsRendering.setSelectedItem(promptEachTimeOpt);
- }
+ setupOutputCombo(epsRendering, "EPS_RENDERING");
+ setupOutputCombo(htmlRendering, "HTML_RENDERING");
+ setupOutputCombo(svgRendering, "SVG_RENDERING");
autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
userIdWidth.setEnabled(!autoIdWidth.isSelected());
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
}
/**
+ * A helper method that sets the items and initial selection in a character
+ * rendering option list (Prompt each time/Lineart/Text)
+ *
+ * @param comboBox
+ * @param propertyKey
+ */
+ protected void setupOutputCombo(JComboBox<Object> comboBox,
+ String propertyKey)
+ {
+ comboBox.addItem(promptEachTimeOpt);
+ comboBox.addItem(lineArtOpt);
+ comboBox.addItem(textOpt);
+
+ /*
+ * JalviewJS doesn't support Lineart so force it to Text
+ */
+ String defaultOption = Platform.isJS() ? "Text"
+ : Cache.getDefault(propertyKey, "Prompt each time");
+ if (defaultOption.equalsIgnoreCase("Text"))
+ {
+ comboBox.setSelectedItem(textOpt);
+ }
+ else if (defaultOption.equalsIgnoreCase("Lineart"))
+ {
+ comboBox.setSelectedItem(lineArtOpt);
+ }
+ else
+ {
+ comboBox.setSelectedItem(promptEachTimeOpt);
+ }
+ }
+
+ /**
* Save user selections on the Preferences tabs to the Cache and write out to
* file.
*
*/
Cache.applicationProperties.setProperty("EPS_RENDERING",
((OptionsParam) epsRendering.getSelectedItem()).getCode());
+ Cache.applicationProperties.setProperty("HTML_RENDERING",
+ ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
+ Cache.applicationProperties.setProperty("SVG_RENDERING",
+ ((OptionsParam) svgRendering.getSelectedItem()).getCode());
/*
* Save Connections settings
Cache.applicationProperties.setProperty("PAD_GAPS",
Boolean.toString(padGaps.isSelected()));
- wsPrefs.updateAndRefreshWsMenuConfig(false);
+ if (!Platform.isJS())
+ {
+ wsPrefs.updateAndRefreshWsMenuConfig(false);
+ }
/*
* Save Backups settings
@Override
public void startupFileTextfield_mouseClicked()
{
+ // TODO: JAL-3048 not needed for Jalview-JS
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
JalviewFileChooser chooser = JalviewFileChooser
.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
{
try
{
- wsPrefs.updateWsMenuConfig(true);
- wsPrefs.refreshWs_actionPerformed(e);
+ if (!Platform.isJS())
+ {
+ wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
+ }
frame.setClosed(true);
} catch (Exception ex)
{
@Override
public void defaultBrowser_mouseClicked(MouseEvent e)
{
- JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle(
- MessageManager.getString("label.select_default_browser"));
+ // TODO: JAL-3048 not needed for j2s
+ if (!Platform.isJS()) // BH 2019
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ JFileChooser chooser = new JFileChooser(".");
+ chooser.setDialogTitle(
+ MessageManager.getString("label.select_default_browser"));
- int value = chooser.showOpenDialog(this);
+ int value = chooser.showOpenDialog(this);
- if (value == JFileChooser.APPROVE_OPTION)
- {
- defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ }
}
-
}
/*
@Override
public void minColour_actionPerformed(JPanel panel)
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_colour_minimum_value"),
- minColour.getBackground());
- if (col != null)
- {
- panel.setBackground(col);
- }
- panel.repaint();
+ panel);
}
@Override
public void maxColour_actionPerformed(JPanel panel)
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_colour_maximum_value"),
- maxColour.getBackground());
- if (col != null)
- {
- panel.setBackground(col);
- }
- panel.repaint();
+ panel);
}
@Override
{
if (!useLegacyGap.isSelected())
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_gap_colour"),
- gapColour.getBackground());
- if (col != null)
- {
- gap.setBackground(col);
- }
- gap.repaint();
+ gap);
}
}
@Override
public void hiddenColour_actionPerformed(JPanel hidden)
{
- Color col = JColorChooser.showDialog(this,
+ JalviewColourChooser.showColourChooser(this,
MessageManager.getString("label.select_hidden_colour"),
- hiddenColour.getBackground());
- if (col != null)
- {
- hidden.setBackground(col);
- }
- hidden.repaint();
+ hidden);
}
@Override
}
} catch (NumberFormatException x)
{
+ userIdWidth.setText("");
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager
.getString("warn.user_defined_width_requirements"),
MessageManager.getString("label.invalid_id_column_width"),
JvOptionPane.WARNING_MESSAGE);
- userIdWidth.setText("");
}
}
*/
protected JComboBox<Object> epsRendering = new JComboBox<>();
+ protected JComboBox<Object> htmlRendering = new JComboBox<>();
+
+ protected JComboBox<Object> svgRendering = new JComboBox<>();
+
protected JLabel userIdWidthlabel = new JLabel();
protected JCheckBox autoIdWidth = new JCheckBox();
*/
protected JPanel wsTab = new JPanel();
+ protected JPanel slivkaTab = new JPanel();
+
/*
* Backups tab components
* a lot of these are member variables instead of local variables only so that they
tabbedPane.add(initConnectionsTab(),
MessageManager.getString("label.connections"));
- tabbedPane.add(initBackupsTab(),
- MessageManager.getString("label.backups"));
+ if (!Platform.isJS())
+ {
+ tabbedPane.add(initBackupsTab(),
+ MessageManager.getString("label.backups"));
+ }
tabbedPane.add(initLinksTab(),
MessageManager.getString("label.urllinks"));
/*
* See WsPreferences for the real work of configuring this tab.
*/
- wsTab.setLayout(new BorderLayout());
- tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
- slivkaTab.setLayout(new BorderLayout());
- tabbedPane.add(slivkaTab, "Slivka Services");
+ if (!Platform.isJS())
+ {
+ wsTab.setLayout(new BorderLayout());
+ tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
++ slivkaTab.setLayout(new BorderLayout());
++ tabbedPane.add(slivkaTab, "Slivka Services");
+ }
/*
* Handler to validate a tab before leaving it - currently only for
/*
* path to Cygwin binaries folder (for Windows)
*/
- if (Platform.isWindows())
+ if (Platform.isWindowsAndNotJS())
{
JLabel cygwinLocation = new JLabel(
MessageManager.getString("label.cygwin_location"));
{
JPanel outputTab = new JPanel();
outputTab.setLayout(null);
- JLabel epsLabel = new JLabel();
+
+ JLabel epsLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "EPS"));
epsLabel.setFont(LABEL_FONT);
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
- epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+ epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
epsRendering.setFont(LABEL_FONT);
- epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+ epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
+ JLabel htmlLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "HTML"));
+ htmlLabel.setFont(LABEL_FONT);
+ htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
+ htmlRendering.setFont(LABEL_FONT);
+ htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
+ JLabel svgLabel = new JLabel(
+ MessageManager.formatMessage("label.rendering_style", "SVG"));
+ svgLabel.setFont(LABEL_FONT);
+ svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
+ svgRendering.setFont(LABEL_FONT);
+ svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
+
JLabel jLabel1 = new JLabel();
jLabel1.setFont(LABEL_FONT);
jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
jLabel1.setText(MessageManager.getString("label.append_start_end"));
jLabel1.setFont(LABEL_FONT);
+
fastajv.setFont(LABEL_FONT);
fastajv.setHorizontalAlignment(SwingConstants.LEFT);
clustaljv.setText(MessageManager.getString("label.clustal") + " ");
TitledBorder titledBorder2 = new TitledBorder(
MessageManager.getString("label.file_output"));
jPanel11.setBorder(titledBorder2);
- jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+ jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
GridLayout gridLayout3 = new GridLayout();
jPanel11.setLayout(gridLayout3);
gridLayout3.setRows(8);
MessageManager.getString("label.automatically_set_id_width"));
autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
.getString("label.adjusts_width_generated_eps_png")));
- autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
+ autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
autoIdWidth.addActionListener(new ActionListener()
{
userIdWidthlabel.setToolTipText(
JvSwingUtils.wrapTooltip(true, MessageManager.getString(
"label.manually_specify_width_left_column")));
- userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
+ userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
userIdWidth.setText("");
- userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
+ userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
userIdWidth.addActionListener(new ActionListener()
{
modellerOutput.setFont(LABEL_FONT);
modellerOutput
.setText(MessageManager.getString("label.use_modeller_output"));
- modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+ modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
embbedBioJSON.setFont(LABEL_FONT);
embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
- embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
+ embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
jPanel11.add(jLabel1);
jPanel11.add(blcjv);
outputTab.add(userIdWidth);
outputTab.add(userIdWidthlabel);
outputTab.add(modellerOutput);
- outputTab.add(embbedBioJSON);
- outputTab.add(epsLabel);
- outputTab.add(epsRendering);
+ if (!Platform.isJS())
+ {
+ /*
+ * JalviewJS doesn't support Lineart option or SVG output
+ */
+ outputTab.add(embbedBioJSON);
+ outputTab.add(epsLabel);
+ outputTab.add(epsRendering);
+ outputTab.add(htmlLabel);
+ outputTab.add(htmlRendering);
+ outputTab.add(svgLabel);
+ outputTab.add(svgRendering);
+ }
outputTab.add(jPanel11);
return outputTab;
}
docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
structureTab.add(docFieldPref);
+ /*
+ * hide Chimera options in JalviewJS
+ */
+ if (Platform.isJS())
+ {
+ pathLabel.setVisible(false);
+ chimeraPath.setVisible(false);
+ viewerLabel.setVisible(false);
+ structViewer.setVisible(false);
+ }
+
return structureTab;
}
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
+
+ if (Platform.isJS())
+ {
+ startupCheckbox.setVisible(false);
+ startupFileTextfield.setVisible(false);
+ }
+
return visualTab;
}
BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
.getSavedBackupEntry();
enableBackupFiles
- .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
+ .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
.createBackupFilesPresetEntry(Cache
{
try
{
- i = Integer.parseInt((String) s.getValue());
+ i = ((Integer) s.getValue()).intValue();
} catch (Exception e)
{
Cache.log.error(
{
max = def;
}
+ if (def < min)
+ {
+ def = min;
+ }
SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
s.setModel(sModel);
import jalview.bin.Cache;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
- import jalview.ws.WSMenuEntryProviderI;
+ import jalview.ws.WSDiscovererI;
import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ParamDatastoreI;
* @author JimP
*
*/
- public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
+ public class Jws2Discoverer implements WSDiscovererI, Runnable
{
public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws";
} catch (Exception e)
{
}
- ;
for (JabaWsServerQuery squery : qrys)
{
if (squery.isRunning())
alignFrame, typeFilter);
}
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
if (args.length > 0)
{
testUrls.add(url);
}
- ;
}
Thread runner = getDiscoverer()
.startDiscoverer(new PropertyChangeListener()
} catch (InterruptedException e)
{
}
- ;
}
try
{
return discoverer;
}
+ @Override
public boolean hasServices()
{
return !running && services != null && services.size() > 0;
}
+ @Override
public boolean isRunning()
{
return running;
}
+ @Override
public void setServiceUrls(List<String> wsUrls)
{
if (wsUrls != null && !wsUrls.isEmpty())
*
* @return
*/
+ @Override
public List<String> getServiceUrls()
{
if (testUrls != null)
return urls;
}
+ @Override
public Vector<ServiceWithParameters> getServices()
{
return (services == null) ? new Vector<>()
* @param foo
* @return
*/
- public static boolean testServiceUrl(URL foo)
+ @Override
+ public boolean testServiceUrl(URL foo)
{
try
{
* @param changeSupport2
* @return new thread
*/
+ @Override
public Thread startDiscoverer(PropertyChangeListener changeSupport2)
{
/* if (restart())
* @return a human readable report of any problems with the service URLs used
* for discovery
*/
+ @Override
public String getErrorMessages()
{
if (!isRunning() && !isAborted())
return null;
}
+ @Override
public int getServerStatusFor(String url)
{
if (validServiceUrls != null && validServiceUrls.contains(url))
{
- return 1;
+ return STATUS_OK;
}
if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
{
- return 0;
+ return STATUS_NO_SERVICES;
}
if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
{
- return -1;
+ return STATUS_INVALID;
}
- return -2;
+ return STATUS_UNKNOWN;
}
/**
git://source.jalview.org / jalview.git / commitdiff