import jalview.analysis.AlignmentUtils;
import jalview.analysis.CrossRef;
import jalview.analysis.Dna;
+import jalview.analysis.GeneticCodeI;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
-import jalview.api.AlignExportSettingI;
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignFrameI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+//from JalviewLite imports import jalview.api.FeatureRenderer;
import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.SplitContainerI;
import jalview.api.ViewStyleI;
import jalview.api.analysis.SimilarityParamsI;
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.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
+import jalview.io.BackupFiles;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
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.dialogrunner.RunResponse;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.ws.DBRefFetcher;
import jalview.ws.seqfetcher.DbSourceProxy;
import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Component;
+import java.awt.Dimension;
import java.awt.Rectangle;
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintWriter;
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.JFileChooser;
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;
+
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
-public class AlignFrame extends GAlignFrame implements DropTargetListener,
- IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener,
- PropertyChangeListener
+@SuppressWarnings("serial")
+public class AlignFrame extends GAlignFrame
+ implements AlignFrameI, DropTargetListener, IProgressIndicator,
+ AlignViewControllerGuiI, ColourChangeListener
{
public static final int DEFAULT_WIDTH = 700;
viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
- alignPanel = new AlignmentPanel(this, viewport);
-
- addAlignmentPanel(alignPanel, true);
init();
}
{
viewport.hideSequence(hiddenSeqs);
}
- alignPanel = new AlignmentPanel(this, viewport);
- addAlignmentPanel(alignPanel, true);
init();
}
{
viewport = ap.av;
alignPanel = ap;
- addAlignmentPanel(ap, false);
init();
}
- @Override
- public void propertyChange(PropertyChangeEvent evt)
- {
- Desktop.getDesktop().propertyChange(evt);
- }
-
-
- /**
- * BH 2018
- *
- * @return true if we have any features
- */
- @Override
- protected boolean haveAlignmentFeatures() {
- AlignmentI alignment = getViewport().getAlignment();
-
- for (int i = 0; i < alignment.getHeight(); i++)
- {
- SequenceI seq = alignment.getSequenceAt(i);
- for (String group : seq.getFeatures().getFeatureGroups(true))
- {
- if (group != null)return true;
- }
- }
- return false;
- }
-
/**
* initalise the alignframe from the underlying viewport data and the
* configurations
*/
void init()
{
+ boolean newPanel = (alignPanel == null);
+ viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ if (newPanel)
+ {
+ if (Platform.isJS())
+ {
+ // need to set this up front if NOANNOTATION is
+ // used in conjunction with SHOWOVERVIEW.
+
+ // I have not determined if this is appropriate for
+ // Jalview/Java, as it means we are setting this flag
+ // for all subsequent AlignFrames. For now, at least,
+ // I am setting it to be JalviewJS-only.
+
+ boolean showAnnotation = Jalview.getInstance().getShowAnnotation();
+ viewport.setShowAnnotation(showAnnotation);
+ }
+ alignPanel = new AlignmentPanel(this, viewport);
+ }
+ addAlignmentPanel(alignPanel, newPanel);
+
+ // setBackground(Color.white); // BH 2019
+
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ // JalviewJS options
+ statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+ alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
}
avc = new jalview.controller.AlignViewController(this, viewport,
// modifyPID.setEnabled(false);
}
- String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+ String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT,
"No sort");
if (sortby.equals("Id"))
sortPairwiseMenuItem_actionPerformed(null);
}
- this.alignPanel.av
- .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
-
setMenusFromViewport(viewport);
buildSortByAnnotationScoresMenu();
calculateTree.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
});
buildColourMenu();
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
- /**
- * BH 2018 ignore service listeners
- *
- * @j2sNative
- *
- */
+ if (!Platform.isJS())
{
- addServiceListeners();
+ addServiceListeners();
}
setGUINucleotide();
}
wrapMenuItem_actionPerformed(null);
}
- if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+ if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
{
this.overviewMenuItem_actionPerformed(null);
}
new ViewSetProvider()
{
+
@Override
public AlignmentPanel[] getAllAlignmentPanels()
{
}, selviews, new ItemListener()
{
+
@Override
public void itemStateChanged(ItemEvent e)
{
}
addFocusListener(new FocusAdapter()
{
+
@Override
public void focusGained(FocusEvent e)
{
setFileFormat(format);
reload.setEnabled(true);
}
-
+
/**
* 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) {
+ public void setFileObject(File file)
+ {
this.fileObject = file;
}
{
addKeyListener(new KeyAdapter()
{
+
@Override
public void keyPressed(KeyEvent evt)
{
switch (evt.getKeyCode())
{
- case 27: // escape key
- deselectAllSequenceMenuItem_actionPerformed(null);
-
+ case KeyEvent.VK_ESCAPE: // escape key
+ // alignPanel.deselectAllSequences();
+ alignPanel.deselectAllSequences();
break;
case KeyEvent.VK_DOWN:
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)
}
}
+
@Override
public void keyReleased(KeyEvent evt)
{
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
- if (aSize == 1 && ap.av.viewName == null)
+ if (aSize == 1 && ap.av.getViewName() == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName, ap);
+ tabbedPane.addTab(ap.av.getViewName(), ap);
ap.setVisible(false);
}
{
ap.av.getAlignment().padGaps();
}
- ap.av.updateConservation(ap);
- ap.av.updateConsensus(ap);
- ap.av.updateStrucConsensus(ap);
+ if (Jalview.getInstance().getStartCalculations())
+ {
+ ap.av.updateConservation(ap);
+ ap.av.updateConsensus(ap);
+ ap.av.updateStrucConsensus(ap);
+ }
}
}
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
- tabbedPane.addTab(first.av.viewName, first);
+ tabbedPane.addTab(first.av.getViewName(), first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
private void addServiceListeners()
{
final java.beans.PropertyChangeListener thisListener;
- Desktop.instance.addJalviewPropertyChangeListener("services",
+ Desktop.getInstance().addJalviewPropertyChangeListener("services",
thisListener = new java.beans.PropertyChangeListener()
{
+
@Override
public void propertyChange(PropertyChangeEvent evt)
{
SwingUtilities.invokeLater(new Runnable()
{
+
@Override
public void run()
{
});
addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
{
+
@Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
// System.out.println("deregistering discoverer listener");
- Desktop.instance.removeJalviewPropertyChangeListener("services",
- thisListener);
+ Desktop.getInstance().removeJalviewPropertyChangeListener(
+ "services", thisListener);
closeMenuItem_actionPerformed(true);
- };
+ }
});
// Finally, build the menu once to get current service state
new Thread(new Runnable()
{
+
@Override
public void run()
{
* operation that affects the data in the current view (selection changed,
* etc) to update the menus to reflect the new state.
*/
+
@Override
public void setMenusForViewport()
{
* @param av
* AlignViewport
*/
- void setMenusFromViewport(AlignViewport av)
+ public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
scaleLeft.setVisible(av.getWrapAlignment());
scaleRight.setVisible(av.getWrapAlignment());
annotationPanelMenuItem.setState(av.isShowAnnotation());
- /*
- * Show/hide annotations only enabled if annotation panel is shown
- */
- showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
- showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
- hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+ // Show/hide annotations only enabled if annotation panel is shown
+ syncAnnotationMenuItems(av.isShowAnnotation());
viewBoxesMenuItem.setSelected(av.getShowBoxes());
viewTextMenuItem.setSelected(av.getShowText());
showNonconservedMenuItem.setSelected(av.getShowUnconserved());
applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
showDbRefsMenuitem.setSelected(av.isShowDBRefs());
- autoCalculate.setSelected(av.autoCalculateConsensus);
+ autoCalculate
+ .setSelected(av.getAutoCalculateConsensusAndConservation());
sortByTree.setSelected(av.sortByTree);
listenToViewSelections.setSelected(av.followSelection);
*
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
+
@Override
public void setProgressBar(String message, long id)
{
progressBar.setProgressBar(message, id);
}
+
@Override
public void registerHandler(final long id,
final IProgressIndicatorHandler handler)
*
* @return true if any progress bars are still active
*/
+
@Override
public boolean operationInProgress()
{
return progressBar.operationInProgress();
}
+ /**
+ * Sets the text of the status bar. Note that setting a null or empty value
+ * will cause the status bar to be hidden, with possibly undesirable flicker
+ * of the screen layout.
+ */
+
@Override
public void setStatus(String text)
{
- statusBar.setText(text);
+ statusBar.setText(text == null || text.isEmpty() ? " " : text);
}
/*
return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
}
+
@Override
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
- new jalview.gui.SequenceFetcher(this);
+ new SequenceFetcher(this);
}
+
@Override
public void addFromFile_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
+ Desktop.getInstance().inputLocalFileMenuItem_actionPerformed(viewport);
}
+
@Override
public void reload_actionPerformed(ActionEvent e)
{
- if (fileName != null)
+ if (fileName == null)
{
- // TODO: JAL-1108 - ensure all associated frames are closed regardless of
- // originating file's format
- // TODO: work out how to recover feature settings for correct view(s) when
- // file is reloaded.
- if (FileFormat.Jalview.equals(currentFileFormat))
+ return;
+ }
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
+ // TODO: work out how to recover feature settings for correct view(s) when
+ // file is reloaded.
+ if (FileFormat.Jalview.equals(currentFileFormat))
+ {
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ for (int i = 0; i < frames.length; i++)
{
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- for (int i = 0; i < frames.length; i++)
+ if (frames[i] instanceof AlignFrame && frames[i] != this
+ && ((AlignFrame) frames[i]).fileName != null
+ && ((AlignFrame) frames[i]).fileName.equals(fileName))
{
- if (frames[i] instanceof AlignFrame && frames[i] != this
- && ((AlignFrame) frames[i]).fileName != null
- && ((AlignFrame) frames[i]).fileName.equals(fileName))
+ try
+ {
+ frames[i].setSelected(true);
+ Desktop.getInstance().closeAssociatedWindows();
+ } catch (java.beans.PropertyVetoException ex)
{
- try
- {
- frames[i].setSelected(true);
- Desktop.instance.closeAssociatedWindows();
- } catch (java.beans.PropertyVetoException ex)
- {
- }
}
-
}
- Desktop.instance.closeAssociatedWindows();
- FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
- ? DataSourceType.URL : DataSourceType.FILE;
- loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
}
- else
- {
- Rectangle bounds = this.getBounds();
+ Desktop.getInstance().closeAssociatedWindows();
- FileLoader loader = new FileLoader();
+ FileLoader loader = new FileLoader();
+ DataSourceType protocol = fileName.startsWith("http:")
+ ? DataSourceType.URL
+ : DataSourceType.FILE;
+ loader.loadFile(viewport,
+ (fileObject == null ? fileName : fileObject), protocol,
+ currentFileFormat);
+ }
+ else
+ {
+ Rectangle bounds = this.getBounds();
- AlignFrame newframe = null;
+ FileLoader loader = new FileLoader();
- if (fileObject == null)
- {
+ AlignFrame newframe = null;
- DataSourceType protocol = (fileName.startsWith("http:")
- ? DataSourceType.URL : DataSourceType.FILE);
- newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
- currentFileFormat);
- }
- else
- {
- newframe = loader.LoadFileWaitTillLoaded(fileObject, DataSourceType.FILE, currentFileFormat);
- }
+ if (fileObject == null)
+ {
- newframe.setBounds(bounds);
- if (featureSettings != null && featureSettings.isShowing())
+ 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())
+ {
+ final Rectangle fspos = featureSettings.frame.getBounds();
+ // TODO: need a 'show feature settings' function that takes bounds -
+ // need to refactor Desktop.addFrame
+ newframe.featureSettings_actionPerformed(null);
+ final FeatureSettings nfs = newframe.featureSettings;
+ SwingUtilities.invokeLater(new Runnable()
{
- final Rectangle fspos = featureSettings.frame.getBounds();
- // TODO: need a 'show feature settings' function that takes bounds -
- // need to refactor Desktop.addFrame
- newframe.featureSettings_actionPerformed(null);
- final FeatureSettings nfs = newframe.featureSettings;
- SwingUtilities.invokeLater(new Runnable()
+
+ @Override
+ public void run()
{
- @Override
- public void run()
- {
- nfs.frame.setBounds(fspos);
- }
- });
- this.featureSettings.close();
- this.featureSettings = null;
- }
- this.closeMenuItem_actionPerformed(true);
+ nfs.frame.setBounds(fspos);
+ }
+ });
+ this.featureSettings.close();
+ this.featureSettings = null;
}
+ this.closeMenuItem_actionPerformed(true);
}
}
+
@Override
public void addFromText_actionPerformed(ActionEvent e)
{
- Desktop.instance
+ Desktop.getInstance()
.inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
}
+
@Override
public void addFromURL_actionPerformed(ActionEvent e)
{
- Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
+ Desktop.getInstance().inputURLMenuItem_actionPerformed(viewport);
}
+
@Override
public void save_actionPerformed(ActionEvent e)
{
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();
- final JalviewFileChooser chooser = JalviewFileChooser
+ JalviewFileChooser chooser = JalviewFileChooser
.forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
- final AlignFrame us = this;
+
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(
MessageManager.getString("label.save_alignment_to_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
- chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ int value = chooser.showSaveDialog(this);
+
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
- @Override
- public void run()
- {
- currentFileFormat = chooser.getSelectedFormat();
- 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();
- chooser.showSaveDialog(us);
- }
+ return;
+ }
+ currentFileFormat = chooser.getSelectedFormat();
+ // todo is this (2005) test now obsolete - value is never null?
+ while (currentFileFormat == null)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ 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;
+ }
+ }
+
+ fileName = chooser.getSelectedFile().getPath();
- fileName = chooser.getSelectedFile().getPath();
+ Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
+ Cache.setProperty("LAST_DIRECTORY", fileName);
+ saveAlignment(fileName, currentFileFormat);
+ }
- Cache.setProperty("DEFAULT_FILE_FORMAT",
- currentFileFormat.getName());
+ boolean lastSaveSuccessful = false;
- Cache.setProperty("LAST_DIRECTORY", fileName);
- saveAlignment(fileName, currentFileFormat);
- }
- }).showSaveDialog(this);
+ FileFormatI lastFormatSaved;
+
+ String lastFilenameSaved;
+
+ /**
+ * Raise a dialog or status message for the last call to saveAlignment.
+ *
+ * @return true if last call to saveAlignment(file, format) was successful.
+ */
+ public boolean isSaveAlignmentSuccessful()
+ {
+
+ if (!lastSaveSuccessful)
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }),
+ MessageManager.getString("label.error_saving_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+
+ setStatus(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format", new Object[]
+ { lastFilenameSaved, lastFormatSaved }));
+
+ }
+ return lastSaveSuccessful;
}
- public boolean saveAlignment(String file, FileFormatI format)
+ /**
+ * Saves the alignment to the specified file path, in the specified format,
+ * which may be an alignment format, or Jalview project format. If the
+ * alignment has hidden regions, or the format is one capable of including
+ * non-sequence data (features, annotations, groups), then the user may be
+ * prompted to specify what to include in the output.
+ *
+ * @param file
+ * @param format
+ */
+ public void saveAlignment(String file, FileFormatI format)
{
- boolean success = true;
+ lastSaveSuccessful = true;
+ lastFilenameSaved = file;
+ lastFormatSaved = format;
if (FileFormat.Jalview.equals(format))
{
String shortName = title;
-
- if (shortName.indexOf(java.io.File.separatorChar) > -1)
+ if (shortName.indexOf(File.separatorChar) > -1)
{
- shortName = shortName.substring(
- shortName.lastIndexOf(java.io.File.separatorChar) + 1);
+ shortName = shortName
+ .substring(shortName.lastIndexOf(File.separatorChar) + 1);
}
-
- success = new 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()
{
- try
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport
+ .getAlignExportData(options);
+ String output = new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns());
+ if (output == null)
{
- PrintWriter out = new PrintWriter(new FileWriter(file));
-
- out.print(output);
- out.close();
- this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format.getName() }));
- } catch (Exception ex)
+ lastSaveSuccessful = false;
+ }
+ else
{
- success = false;
- ex.printStackTrace();
+ // 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();
+ AlignFrame.this.setTitle(file);
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format.getName() }));
+ lastSaveSuccessful = true;
+ } catch (Exception ex)
+ {
+ lastSaveSuccessful = false;
+ ex.printStackTrace();
+ }
+
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ // do the backup file roll and rename the temp file to actual file
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ }
}
}
- }
+ };
- if (!success)
+ /*
+ * show dialog with export options if applicable; else just do it
+ */
+ if (AlignExportOptions.isNeeded(viewport, format))
{
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { fileName }),
- MessageManager.getString("label.error_saving_file"),
- JvOptionPane.WARNING_MESSAGE);
+ AlignExportOptions choices = new AlignExportOptions(
+ alignPanel.getAlignViewport(), format, options);
+ choices.setResponseAction(0, outputAction);
+ choices.setResponseAction(1, cancelAction);
+ choices.showDialog();
+ }
+ else
+ {
+ outputAction.run();
}
-
- return success;
}
/**
- * 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)
+ .forName(fileFormatName);
+ AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
+ Runnable outputAction = new Runnable()
{
- new OOMWarning("Outputting alignment as " + e.getActionCommand(),
- oom);
- cap.dispose();
- }
-
- }
-
- public static AlignmentExportData getAlignmentForExport(
- FileFormatI format, AlignViewportI viewport,
- AlignExportSettingI exportSettings)
- {
- AlignmentI alignmentToExport = null;
- AlignExportSettingI settings = exportSettings;
- String[] omitHidden = null;
-
- HiddenSequences hiddenSeqs = viewport.getAlignment()
- .getHiddenSequences();
-
- alignmentToExport = viewport.getAlignment();
-
- boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
- if (settings == null)
- {
- settings = new AlignExportSettings(hasHiddenSeqs,
- viewport.hasHiddenColumns(), format);
- }
- // settings.isExportAnnotations();
-
- if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
- {
- omitHidden = viewport.getViewAsString(false,
- settings.isExportHiddenSequences());
- }
+
+ @Override
+ public void run()
+ {
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport
+ .getAlignExportData(options);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ try
+ {
+ FileFormatI format = fileFormat;
+ cap.setText(new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { fileFormat.getName() }), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + fileFormat.getName(),
+ oom);
+ cap.dispose();
+ }
+ }
+ };
- int[] alignmentStartEnd = new int[2];
- if (hasHiddenSeqs && settings.isExportHiddenSequences())
+ /*
+ * show dialog with export options if applicable; else just do it
+ */
+ if (AlignExportOptions.isNeeded(viewport, fileFormat))
{
- alignmentToExport = hiddenSeqs.getFullAlignment();
+ AlignExportOptions choices = new AlignExportOptions(
+ alignPanel.getAlignViewport(), fileFormat, options);
+ choices.setResponseAction(0, outputAction);
+ choices.showDialog();
}
else
{
- alignmentToExport = viewport.getAlignment();
+ outputAction.run();
}
- alignmentStartEnd = viewport.getAlignment().getHiddenColumns()
- .getVisibleStartAndEndIndex(alignmentToExport.getWidth());
- AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
- omitHidden, alignmentStartEnd, settings);
- return ed;
}
/**
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
htmlSVG.exportHTML(null);
}
+
@Override
public void bioJSMenuItem_actionPerformed(ActionEvent e)
{
}
/**
- * 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 pageSetup_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void printMenuItem_actionPerformed(ActionEvent e)
{
thread.start();
}
+
@Override
public void exportFeatures_actionPerformed(ActionEvent e)
{
new AnnotationExporter(alignPanel).exportFeatures();
}
+
@Override
public void exportAnnotations_actionPerformed(ActionEvent e)
{
new AnnotationExporter(alignPanel).exportAnnotations();
}
+
@Override
public void associatedData_actionPerformed(ActionEvent e)
{
- 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"));
-
- Desktop.getDesktop().dialogData = new Object[] { "SelectedFile",
- new Runnable()
- {
-
- @Override
- public void run()
- {
- Object[] data = Desktop.getDesktop().dialogData;
- int value = ((Integer) data[0]).intValue();
-
- if (value == JFileChooser.APPROVE_OPTION)
- {
- JalviewFileChooser chooser = (JalviewFileChooser) data[2];
- String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice, null, null, null);
- }
- }
-
- }, chooser };
-
- chooser.showOpenDialog(null);
-
-
+ String tooltip = MessageManager
+ .getString("label.load_jalview_annotations");
+ chooser.setDialogTitle(tooltip);
+ chooser.setToolTipText(tooltip);
+ chooser.setResponseHandler(0, new Runnable()
+ {
+
+ @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);
}
/**
*
* @param closeAllTabs
*/
+
@Override
public void closeMenuItem_actionPerformed(boolean closeAllTabs)
{
if (closeAllTabs)
{
+ // JalviewJS-develop only
+ //
+ // 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
}
}
+
@Override
public void addHistoryItem(CommandI command)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void redoMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
- protected void copy_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
if (viewport.getSelectionGroup() == null)
{
StringSelection ss = new StringSelection(output);
+ Desktop d = Desktop.getInstance();
try
{
- jalview.gui.Desktop.internalCopy = true;
+ d.internalCopy = true;
// Its really worth setting the clipboard contents
// to empty before setting the large StringSelection!!
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(""), null);
Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
- Desktop.instance);
+ Desktop.getInstance());
} catch (OutOfMemoryError er)
{
new OOMWarning("copying region", er);
hiddenCutoff, hiddenOffset);
}
- Desktop.jalviewClipboard = new Object[] { seqs,
+ d.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() }));
}
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void pasteNew_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void pasteThis_actionPerformed(ActionEvent e)
{
boolean annotationAdded = false;
AlignmentI alignment = null;
- if (Desktop.jalviewClipboard != null)
+ Desktop d = Desktop.getInstance();
+
+ if (d.jalviewClipboard != null)
{
// The clipboard was filled from within Jalview, we must use the
// sequences
// And dataset from the copied alignment
- SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
+ SequenceI[] newseq = (SequenceI[]) d.jalviewClipboard[0];
// be doubly sure that we create *new* sequence objects.
sequences = new SequenceI[newseq.length];
for (int i = 0; i < newseq.length; i++)
if (newAlignment)
{
- if (Desktop.jalviewClipboard != null)
+ if (d.jalviewClipboard != null)
{
// dataset is inherited
- alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
+ alignment.setDataset((Alignment) d.jalviewClipboard[1]);
}
else
{
alignment = viewport.getAlignment();
alwidth = alignment.getWidth() + 1;
// decide if we need to import sequences from an existing dataset
- boolean importDs = Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[1] != alignment.getDataset();
+ boolean importDs = d.jalviewClipboard != null
+ && d.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++)
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
newGraphGroups.add(q, null);
}
newGraphGroups.set(newann.graphGroup,
- new Integer(++fgroup));
+ Integer.valueOf(++fgroup));
}
newann.graphGroup = newGraphGroups.get(newann.graphGroup)
.intValue();
{
// propagate alignment changed.
- viewport.getRanges().setEndSeq(alignment.getHeight());
+ viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
if (annotationAdded)
{
// Duplicate sequence annotation in all views.
DEFAULT_HEIGHT);
String newtitle = new String("Copied sequences");
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
}
+
@Override
protected void expand_newalign(ActionEvent e)
{
DEFAULT_HEIGHT);
String newtitle = new String("Flanking alignment");
- if (Desktop.jalviewClipboard != null
- && Desktop.jalviewClipboard[2] != null)
+ Desktop d = Desktop.getInstance();
+
+ if (d.jalviewClipboard != null && d.jalviewClipboard[2] != null)
{
- HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+ HiddenColumns hc = (HiddenColumns) d.jalviewClipboard[2];
af.viewport.setHiddenColumns(hc);
}
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Action Cut (delete and copy) the selected region
*/
+
@Override
- protected void cut_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed()
{
- copy_actionPerformed(null);
- delete_actionPerformed(null);
+ copy_actionPerformed();
+ delete_actionPerformed();
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Performs menu option to Delete the currently selected region
*/
+
@Override
- protected void delete_actionPerformed(ActionEvent evt)
+ protected void delete_actionPerformed()
{
SequenceGroup sg = viewport.getSelectionGroup();
return;
}
- /*
- * If the cut affects all sequences, warn, remove highlighted columns
- */
- if (sg.getSize() == viewport.getAlignment().getHeight())
+ Runnable okAction = new Runnable()
{
- boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes())
- + 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (isEntireAlignWidth)
+
+ @Override
+ public void run()
{
- int confirm = JvOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JvOptionPane.OK_CANCEL_OPTION);
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
- if (confirm == JvOptionPane.CANCEL_OPTION
- || confirm == JvOptionPane.CLOSED_OPTION)
+ 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)
{
- return;
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
}
}
- viewport.getColumnSelection().removeElements(sg.getStartRes(),
- sg.getEndRes() + 1);
- }
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
+ };
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
-
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
+ /*
+ * If the cut affects all sequences, prompt for confirmation
+ */
+ boolean wholeHeight = sg.getSize() == viewport.getAlignment()
+ .getHeight();
+ boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
+ + 1) == viewport.getAlignment().getWidth()) ? true : false;
+ if (wholeHeight && wholeWidth)
+ {
+ JvOptionPane dialog = JvOptionPane
+ .newOptionDialog(Desktop.getDesktopPane());
+ dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+ Object[] options = new Object[] {
+ MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ dialog.showDialog(MessageManager.getString("warn.delete_all"),
+ MessageManager.getString("label.delete_all"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ }
+ else
{
- try
- {
- this.setClosed(true);
- } catch (Exception ex)
- {
- }
+ okAction.run();
}
}
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void deleteGroups_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- SequenceGroup sg = new SequenceGroup();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
-
- sg.setEndRes(viewport.getAlignment().getWidth() - 1);
- viewport.setSelectionGroup(sg);
- viewport.sendSelection();
- // JAL-2034 - should delegate to
- // alignPanel to decide if overview needs
- // updating.
- alignPanel.paintAlignment(false, false);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ // SequenceGroup sg = new SequenceGroup(
+ // viewport.getAlignment().getSequences());
+ //
+ // sg.setEndRes(viewport.getAlignment().getWidth() - 1);
+ // viewport.setSelectionGroup(sg);
+ // viewport.isSelectionGroupChanged(true);
+ // viewport.sendSelection();
+ // // JAL-2034 - should delegate to
+ // // alignPanel to decide if overview needs
+ // // updating.
+ // alignPanel.paintAlignment(false, false);
+ // PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ alignPanel.selectAllSequences();
}
/**
* @param e
* DOCUMENT ME!
*/
+
@Override
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- if (viewport.cursorMode)
- {
- alignPanel.getSeqPanel().keyboardNo1 = null;
- alignPanel.getSeqPanel().keyboardNo2 = null;
- }
- viewport.setSelectionGroup(null);
- viewport.getColumnSelection().clear();
- viewport.setSelectionGroup(null);
- alignPanel.getIdPanel().getIdCanvas().searchResults = null;
- // JAL-2034 - should delegate to
- // alignPanel to decide if overview needs
- // updating.
- alignPanel.paintAlignment(false, false);
- PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
- viewport.sendSelection();
+ alignPanel.deselectAllSequences();
+ // if (viewport.cursorMode)
+ // {
+ // alignPanel.getSeqPanel().keyboardNo1 = null;
+ // alignPanel.getSeqPanel().keyboardNo2 = null;
+ // }
+ // viewport.setSelectionGroup(null);
+ // viewport.getColumnSelection().clear();
+ // viewport.setSelectionGroup(null);
+ // alignPanel.getIdPanel().getIdCanvas().searchResults = null;
+ // // JAL-2034 - should delegate to
+ // // alignPanel to decide if overview needs
+ // // updating.
+ // alignPanel.paintAlignment(false, false);
+ // PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ // viewport.sendSelection();
}
/**
* @param e
* DOCUMENT ME!
*/
+
@Override
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
{
if (sg == null)
{
- selectAllSequenceMenuItem_actionPerformed(null);
+ alignPanel.selectAllSequences();
return;
}
viewport.sendSelection();
}
+
@Override
public void invertColSel_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void remove2RightMenuItem_actionPerformed(ActionEvent e)
{
column, viewport.getAlignment());
}
- statusBar.setText(MessageManager
- .formatMessage("label.removed_columns", new String[]
+ setStatus(MessageManager.formatMessage("label.removed_columns",
+ new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
* @param e
* DOCUMENT ME!
*/
+
@Override
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
addHistoryItem(removeGapCols);
- statusBar.setText(MessageManager
- .formatMessage("label.removed_empty_columns", new Object[]
+ setStatus(MessageManager.formatMessage("label.removed_empty_columns",
+ new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
* @param e
* DOCUMENT ME!
*/
+
@Override
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void padGapsMenuitem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
/**
* Create a new view of the current alignment.
*/
+
@Override
public void newView_actionPerformed(ActionEvent e)
{
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+ AlignmentPanel newap = new jalview.project.Jalview2XML()
+ .copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
newap.av.setGatherViewsHere(false);
- if (viewport.viewName == null)
+ if (viewport.getViewName() == null)
{
- viewport.viewName = MessageManager
- .getString("label.view_name_original");
+ viewport.setViewName(
+ MessageManager.getString("label.view_name_original"));
}
/*
newap.av.setRedoList(viewport.getRedoList());
/*
+ * copy any visualisation settings that are not saved in the project
+ */
+ newap.av.setColourAppliesToAllGroups(
+ viewport.getColourAppliesToAllGroups());
+
+ /*
* Views share the same mappings; need to deregister any new mappings
* created by copyAlignPanel, and register the new reference to the shared
* mappings
newap.refresh(true); // adjust layout of annotations
}
- newap.av.viewName = getNewViewName(viewTitle);
+ newap.av.setViewName(getNewViewName(viewTitle));
addAlignmentPanel(newap, true);
newap.alignmentChanged();
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
- if (!existingNames.contains(ap.av.viewName))
+ if (!existingNames.contains(ap.av.getViewName()))
{
- existingNames.add(ap.av.viewName);
+ existingNames.add(ap.av.getViewName());
}
}
}
/**
* Explode tabbed views into separate windows.
*/
+
@Override
public void expandViews_actionPerformed(ActionEvent e)
{
/**
* Gather views in separate windows back into a tabbed presentation.
*/
+
@Override
public void gatherViews_actionPerformed(ActionEvent e)
{
- Desktop.instance.gatherViews(this);
+ Desktop.getInstance().gatherViews(this);
}
/**
* @param e
* DOCUMENT ME!
*/
+
@Override
public void font_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void seqLimit_actionPerformed(ActionEvent e)
{
alignPanel.paintAlignment(true, false);
}
+
@Override
public void idRightAlign_actionPerformed(ActionEvent e)
{
alignPanel.paintAlignment(false, false);
}
+
@Override
public void centreColumnLabels_actionPerformed(ActionEvent e)
{
*
* @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
*/
+
@Override
protected void followHighlight_actionPerformed()
{
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+ alignPanel.scrollToPosition(viewport.getSearchResults());
}
}
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
alignPanel.updateLayout();
}
+
@Override
public void showAllSeqs_actionPerformed(ActionEvent e)
{
viewport.showAllHiddenSeqs();
}
+
@Override
public void showAllColumns_actionPerformed(ActionEvent e)
{
viewport.sendSelection();
}
+
@Override
public void hideSelSequences_actionPerformed(ActionEvent e)
{
* @param toggleSeqs
* @param toggleCols
*/
- private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
+ protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
{
boolean hide = false;
* jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
* event.ActionEvent)
*/
+
@Override
public void hideAllButSelection_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
* .ActionEvent)
*/
+
@Override
public void hideAllSelection_actionPerformed(ActionEvent e)
{
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
* jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
* ActionEvent)
*/
+
@Override
public void showAllhidden_actionPerformed(ActionEvent e)
{
viewport.sendSelection();
}
+
@Override
public void hideSelColumns_actionPerformed(ActionEvent e)
{
viewport.hideSelectedColumns();
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
+
@Override
public void hiddenMarkers_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void scaleAbove_actionPerformed(ActionEvent e)
{
viewport.setScaleAboveWrapped(scaleAbove.isSelected());
- // TODO: do we actually need to update overview for scale above change ?
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void scaleLeft_actionPerformed(ActionEvent e)
{
viewport.setScaleLeftWrapped(scaleLeft.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void scaleRight_actionPerformed(ActionEvent e)
{
viewport.setScaleRightWrapped(scaleRight.isSelected());
+ alignPanel.updateLayout();
alignPanel.paintAlignment(true, false);
}
* @param e
* DOCUMENT ME!
*/
+
@Override
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void viewTextMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
{
public FeatureSettings featureSettings;
+
@Override
public FeatureSettingsControllerI getFeatureSettingsUI()
{
return featureSettings;
}
+
@Override
public void featureSettings_actionPerformed(ActionEvent e)
{
+ showFeatureSettingsUI();
+ }
+
+
+ public FeatureSettingsControllerI showFeatureSettingsUI()
+ {
if (featureSettings != null)
{
- featureSettings.close();
+ // featureSettings.closeOldSettings();
featureSettings = null;
}
if (!showSeqFeatures.isSelected())
showSeqFeatures_actionPerformed(null);
}
featureSettings = new FeatureSettings(this);
+ return featureSettings;
}
/**
* @param evt
* DOCUMENT ME!
*/
+
@Override
public void showSeqFeatures_actionPerformed(ActionEvent evt)
{
*
* @param e
*/
+
@Override
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
final boolean setVisible = annotationPanelMenuItem.isSelected();
viewport.setShowAnnotation(setVisible);
- this.showAllSeqAnnotations.setEnabled(setVisible);
- this.hideAllSeqAnnotations.setEnabled(setVisible);
- this.showAllAlAnnotations.setEnabled(setVisible);
- this.hideAllAlAnnotations.setEnabled(setVisible);
+ syncAnnotationMenuItems(setVisible);
alignPanel.updateLayout();
}
+ private void syncAnnotationMenuItems(boolean setVisible)
+ {
+ showAllSeqAnnotations.setEnabled(setVisible);
+ hideAllSeqAnnotations.setEnabled(setVisible);
+ showAllAlAnnotations.setEnabled(setVisible);
+ hideAllAlAnnotations.setEnabled(setVisible);
+ }
+
+
@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[]
* @param e
* DOCUMENT ME!
*/
+
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
}
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel);
+
+ // BH 2019.07.26 we allow for an embedded
+ // undecorated overview with defined size
+ frame.setName(Jalview.getAppID("overview"));
+ //
+ Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1);
+ if (dim != null && dim.width == 0)
+ {
+ dim = null; // hidden, not embedded
+ }
+ OverviewPanel overview = new OverviewPanel(alignPanel, dim);
+
frame.setContentPane(overview);
+ if (dim == null)
+ {
+ dim = new Dimension();
+ // was frame.getSize(), but that is 0,0 at this point;
+ }
+ else
+ {
+ // we are imbedding, and so we have an undecorated frame
+ // and we can set the the frame dimensions accordingly.
+ }
+ // allowing for unresizable option using, style="resize:none"
+ boolean resizable = (Platform.getEmbeddedAttribute(frame,
+ "resize") != "none");
Desktop.addInternalFrame(frame, MessageManager
.formatMessage("label.overview_params", new Object[]
- { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
- true, true);
+ { this.getTitle() }), true, dim.width, dim.height, resizable,
+ true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
+
@Override
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
overview.dispose();
alignPanel.setOverviewPanel(null);
- };
+ }
});
if (getKeyListeners().length > 0)
{
alignPanel.setOverviewPanel(overview);
}
+
@Override
public void textColour_actionPerformed()
{
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
+
@Override
public void annotationColour_actionPerformed()
{
new AnnotationColourChooser(viewport, alignPanel);
}
+
@Override
public void annotationColumn_actionPerformed(ActionEvent e)
{
*
* @param selected
*/
+
@Override
public void applyToAllGroups_actionPerformed(boolean selected)
{
* @param name
* the name (not the menu item label!) of the colour scheme
*/
+
@Override
public void changeColour_actionPerformed(String name)
{
* otherwise set the chosen colour scheme (or null for 'None')
*/
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
- viewport.getAlignment(), viewport.getHiddenRepSequences());
+ viewport, viewport.getAlignment(),
+ viewport.getHiddenRepSequences());
changeColour(cs);
}
*
* @param cs
*/
+
@Override
public void changeColour(ColourSchemeI cs)
{
/**
* Show the PID threshold slider panel
*/
+
@Override
protected void modifyPID_actionPerformed()
{
/**
* Show the Conservation slider panel
*/
+
@Override
protected void modifyConservation_actionPerformed()
{
/**
* Action on selecting or deselecting (Colour) By Conservation
*/
+
@Override
public void conservationMenuItem_actionPerformed(boolean selected)
{
/**
* Action on selecting or deselecting (Colour) Above PID Threshold
*/
+
@Override
public void abovePIDThreshold_actionPerformed(boolean selected)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void sortIDMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
}
}
+
@Override
public void autoCalculate_actionPerformed(ActionEvent e)
{
- viewport.autoCalculateConsensus = autoCalculate.isSelected();
- if (viewport.autoCalculateConsensus)
+ viewport.setAutoCalculateConsensusAndConservation(
+ autoCalculate.isSelected());
+ if (viewport.getAutoCalculateConsensusAndConservation())
{
viewport.firePropertyChange("alignment", null,
viewport.getAlignment().getSequences());
}
}
+
@Override
public void sortByTreeOption_actionPerformed(ActionEvent e)
{
viewport.sortByTree = sortByTree.isSelected();
}
+
@Override
protected void listenToViewSelections_actionPerformed(ActionEvent e)
{
{
if (_s.getLength() < sg.getEndRes())
{
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString(
"label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
MessageManager.getString(
frameTitle += " from ";
- if (viewport.viewName != null)
+ if (viewport.getViewName() != null)
{
- frameTitle += viewport.viewName + " of ";
+ frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
- Desktop.addInternalFrame(tp, frameTitle, 600, 500);
+ Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500);
+ Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height);
}
/**
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
sort.add(item);
item.addActionListener(new java.awt.event.ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
* rebuilding in subsequence calls.
*
*/
+
@Override
public void buildSortByAnnotationScoresMenu()
{
{
sortByAnnotScore.removeAll();
// almost certainly a quicker way to do this - but we keep it simple
- Hashtable scoreSorts = new Hashtable();
+ Hashtable<String, String> scoreSorts = new Hashtable<>();
AlignmentAnnotation aann[];
for (SequenceI sqa : viewport.getAlignment().getSequences())
{
}
}
}
- Enumeration labels = scoreSorts.keys();
+ Enumeration<String> labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
- addSortByAnnotScoreMenuItem(sortByAnnotScore,
- (String) labels.nextElement());
+ addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
* closed, and adjust the tree leaf to sequence mapping when the alignment is
* modified.
*/
+
@Override
public void buildTreeSortMenu()
{
final JMenuItem item = new JMenuItem(tp.getTitle());
item.addActionListener(new java.awt.event.ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
* @param e
* DOCUMENT ME!
*/
+
@Override
protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- chooser.response(
- new jalview.util.dialogrunner.RunResponse(JalviewFileChooser.APPROVE_OPTION)
- {
- @Override
- public void run()
- {
- 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);
- }
- }
- }).openDialog(this);
+ chooser.setResponseHandler(0, new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ 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.getDesktopPane(),
+ ex.getMessage(),
+ MessageManager
+ .getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+ fin.getWarningMessage(),
+ MessageManager.getString(
+ "label.possible_problem_with_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ }
+ });
+ chooser.showOpenDialog(this);
}
public TreePanel showNewickTree(NewickFile nf, String treeTitle)
if (nf.getTree() != null)
{
tp = new TreePanel(alignPanel, nf, treeTitle, input);
-
- tp.setSize(w, h);
+ Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1);
+ if (dim == null)
+ {
+ dim = new Dimension(w, h);
+ }
+ else
+ {
+ // no offset, either
+ x = 0;
+ }
+ tp.setSize(dim.width, dim.height);
if (x > 0 && y > 0)
{
tp.setLocation(x, y);
}
- Desktop.addInternalFrame(tp, treeTitle, w, h);
+ Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height);
}
} catch (Exception ex)
{
buildingMenu = true;
new Thread(new Runnable()
{
+
@Override
public void run()
{
final JMenu dismenu = new JMenu("Protein Disorder");
// JAL-940 - only show secondary structure prediction services from
// the legacy server
+ Hashtable<String, Vector<ServiceHandle>> ds = Discoverer
+ .getInstance().getServices();
if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
- // &&
- Discoverer.services != null && (Discoverer.services.size() > 0))
+ // &&
+ ds != null && (ds.size() > 0))
{
// TODO: refactor to allow list of AbstractName/Handler bindings to
// be
// No MSAWS used any more:
// Vector msaws = null; // (Vector)
// Discoverer.services.get("MsaWS");
- Vector secstrpr = (Vector) Discoverer.services
- .get("SecStrPred");
+ Vector<ServiceHandle> secstrpr = ds.get("SecStrPred");
if (secstrpr != null)
{
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
- .get(i);
+ final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
int p = secstrmenu.getItemCount();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+
@Override
public void run()
{
webService.add(me.webServiceNoServices);
}
// TODO: move into separate menu builder class.
- boolean new_sspred = false;
+ // boolean new_sspred = false;
if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
{
- Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
+ Jws2Discoverer jws2servs = Jws2Discoverer.getInstance();
if (jws2servs != null)
{
if (jws2servs.hasServices())
*
* @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
* JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
* AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
*
- * @Override public void actionPerformed(ActionEvent e) {
+ * public void actionPerformed(ActionEvent e) {
* jalview.datamodel.AlignmentView
* .testSelectionViews(af.viewport.getAlignment(),
* af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
JMenuItem xtype = new JMenuItem(source);
xtype.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
* Construct and display a new frame containing the translation of this
* frame's DNA sequences to their aligned protein (amino acid) equivalents.
*/
+
@Override
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
AlignmentI al = null;
try
{
Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
- al = dna.translateCdna();
+ al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
jalview.bin.Cache.log.error(
final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JvOptionPane.ERROR_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg,
+ errorTitle, JvOptionPane.ERROR_MESSAGE);
return;
}
if (al == null || al.getHeight() == 0)
"label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
final String errorTitle = MessageManager
.getString("label.translation_failed");
- JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
- JvOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), msg,
+ errorTitle, JvOptionPane.WARNING_MESSAGE);
}
else
{
af.setFileFormat(this.currentFileFormat);
final String newTitle = MessageManager
.formatMessage("label.translation_of_params", new Object[]
- { this.getTitle() });
+ { this.getTitle(), codeTable.getId() });
af.setTitle(newTitle);
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- viewport.openSplitFrame(af, new Alignment(seqs));
+ AlignViewport.openSplitFrame(this, af, new Alignment(seqs));
}
else
{
*/
public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
{
- // BH 2018
+ // BH 2018
return avc.parseFeaturesFile(file, sourceType,
- Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+ Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false));
}
+
@Override
public void refreshFeatureUI(boolean enableIfNecessary)
{
}
+
@Override
public void dragEnter(DropTargetDragEvent evt)
{
}
+
@Override
public void dragExit(DropTargetEvent evt)
{
}
+
@Override
public void dragOver(DropTargetDragEvent evt)
{
}
+
@Override
public void dropActionChanged(DropTargetDragEvent evt)
{
}
+
@Override
public void drop(DropTargetDropEvent evt)
{
// Java's Transferable for native dnd
evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
Transferable t = evt.getTransferable();
-
-
- final AlignFrame thisaf = this;
+
final List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
try
{
Desktop.transferFromDropTarget(files, protocols, evt, t);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- if (files != null)
+ if (files.size() > 0)
{
new Thread(new Runnable()
{
+
@Override
public void run()
{
+ loadDroppedFiles(files, protocols, evt, t);
+ }
+ }).start();
+ }
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ protected void loadDroppedFiles(List<Object> files,
+ List<DataSourceType> protocols, DropTargetDropEvent evt,
+ Transferable t)
+ {
try
{
// check to see if any of these files have names matching sequences
ArrayList<Object> filesnotmatched = new ArrayList<>();
for (int i = 0; i < files.size(); i++)
{
- // BH 2018
+ // BH 2018
Object file = files.get(i);
String fileName = file.toString();
String pdbfn = "";
- DataSourceType protocol = (file instanceof File ? DataSourceType.FILE : FormatAdapter.checkProtocol(fileName));
+ DataSourceType protocol = (file instanceof File
+ ? DataSourceType.FILE
+ : FormatAdapter.checkProtocol(fileName));
if (protocol == DataSourceType.FILE)
{
- File fl = (file instanceof File ? (File) file : new File(fileName));
+ 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)
int assocfiles = 0;
if (filesmatched.size() > 0)
{
- boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
+ boolean autoAssociate = Cache.getDefault(
+ Preferences.AUTOASSOCIATE_PDBANDSEQS, false);
if (!autoAssociate)
{
String msg = MessageManager.formatMessage(
.toString() });
String ttl = MessageManager.getString(
"label.automatically_associate_structure_files_by_name");
- int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
- ttl, JvOptionPane.YES_NO_OPTION);
+ int choice = JvOptionPane.showConfirmDialog(this, msg, ttl,
+ JvOptionPane.YES_NO_OPTION);
autoAssociate = choice == JvOptionPane.YES_OPTION;
}
if (autoAssociate)
// associating PDB files which have no IDs.
for (SequenceI toassoc : (SequenceI[]) fm[2])
{
- PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq((String) fm[0],
- (DataSourceType) fm[1], toassoc, false,
- Desktop.instance);
+ PDBEntry pe = AssociatePdbFileWithSeq
+ .associatePdbWithSeq(fm[0].toString(),
+ (DataSourceType) fm[1], toassoc, false);
if (pe != null)
{
System.err.println("Associated file : "
- + ((String) fm[0]) + " with "
+ + (fm[0].toString()) + " with "
+ toassoc.getDisplayId(true));
assocfiles++;
}
}
if (filesnotmatched.size() > 0)
{
- if (assocfiles > 0 && (Cache.getDefault(
- "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
- || JvOptionPane.showConfirmDialog(thisaf,
+ if (assocfiles > 0 && (Cache
+ .getDefault("AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
+ || JvOptionPane.showConfirmDialog(this,
"<html>" + MessageManager.formatMessage(
"label.ignore_unmatched_dropped_files_info",
new Object[]
ex.printStackTrace();
}
}
- }).start();
- }
- }
/**
* Attempt to load a "dropped" file or URL string, by testing in turn for
changeColour(
new TCoffeeColourScheme(viewport.getAlignment()));
isAnnotation = true;
- statusBar.setText(MessageManager.getString(
+ setStatus(MessageManager.getString(
"label.successfully_pasted_tcoffee_scores_to_alignment"));
}
else
{
// some problem - if no warning its probable that the ID matching
// process didn't work
- JvOptionPane.showMessageDialog(Desktop.desktop,
+ JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
tcf.getWarningMessage() == null
? MessageManager.getString(
"label.check_file_matches_sequence_ids_alignment")
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))
{
+ SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+ if (splitFrame != null)
+ {
+ splitFrame.repaint();
+ }
+ else
+ {
alignPanel.paintAlignment(true, true);
}
}
+ }
else
{
- new FileLoader().LoadFile(viewport, file, sourceType, format);
+ new FileLoader().loadFile(viewport, file, sourceType, format);
}
}
}
if (isAnnotation)
{
-
- alignPanel.adjustAnnotationHeight();
- viewport.updateSequenceIdColours();
- buildSortByAnnotationScoresMenu();
- alignPanel.paintAlignment(true, true);
+ updateForAnnotations();
}
} catch (Exception ex)
{
+ (format != null
? "(parsing as '" + format + "' file)"
: ""),
- oom, Desktop.desktop);
+ oom, Desktop.getDesktopPane());
+ }
+ }
+
+ /**
+ * Do all updates necessary after an annotation file such as jnet. Also called
+ * from Jalview.loadAppletParams for "annotations", "jnetFile"
+ */
+ public void updateForAnnotations()
+ {
+ alignPanel.adjustAnnotationHeight();
+ viewport.updateSequenceIdColours();
+ buildSortByAnnotationScoresMenu();
+ alignPanel.paintAlignment(true, true);
+ }
+
+ /**
+ * Change the display state for the given feature groups -- Added by BH from
+ * JalviewLite
+ *
+ * @param groups
+ * list of group strings
+ * @param state
+ * visible or invisible
+ */
+
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ jalview.api.FeatureRenderer fr = null;
+ viewport.setShowSequenceFeatures(true);
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+
+ fr.setGroupVisibility(Arrays.asList(groups), state);
+ alignPanel.getSeqPanel().seqCanvas.repaint();
+ if (alignPanel.overviewPanel != null)
+ {
+ alignPanel.overviewPanel.updateOverviewImage();
+ }
}
}
* Method invoked by the ChangeListener on the tabbed pane, in other words
* when a different tabbed pane is selected by the user or programmatically.
*/
+
@Override
public void tabSelectionChanged(int index)
{
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();
+ }
+ }
+
}
/*
/**
* On right mouse click on view tab, prompt for and set new view name.
*/
+
@Override
public void tabbedPane_mousePressed(MouseEvent e)
{
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)
{
- viewport.viewName = reply;
+ viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
/**
* Open the dialog for regex description parsing.
*/
+
@Override
protected void extractScores_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
* )
*/
+
@Override
protected void showDbRefs_actionPerformed(ActionEvent e)
{
* @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
* ActionEvent)
*/
+
@Override
protected void showNpFeats_actionPerformed(ActionEvent e)
{
Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
trimrs.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
trimrs.setSelected(trimrs.isSelected());
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.valueOf(trimrs.isSelected()).toString());
- };
+ }
});
rfetch.add(trimrs);
JMenuItem fetchr = new JMenuItem(
fetchr.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+
@Override
public void run()
{
alignPanel.alignFrame.featureSettings, isNucleotide);
dbRefFetcher.addListener(new FetchFinishedListenerI()
{
+
@Override
public void finished()
{
+ //
+ // for (FeatureSettingsModelI srcSettings : dbRefFetcher
+ // .getFeatureSettingsModels())
+ // {
+ //
+ // alignPanel.av.mergeFeaturesStyle(srcSettings);
+ // }
AlignFrame.this.setMenusForViewport();
}
});
});
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);
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);
+ jalview.ws.SequenceFetcher
+ sf = jalview.ws.SequenceFetcher.getInstance();
+ 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;
}
if (otherdb.size() == 1)
{
- final DbSourceProxy[] dassource = otherdb
- .toArray(new DbSourceProxy[0]);
DbSourceProxy src = otherdb.get(0);
+ DbSourceProxy[] dassource = new DbSourceProxy[] { src };
fetchr = new JMenuItem(src.getDbSource());
fetchr.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+
@Override
public void run()
{
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
+
@Override
public void finished()
{
+ FeatureSettingsModelI srcSettings = dassource[0]
+ .getFeatureColourScheme();
+ // alignPanel.av.mergeFeaturesStyle(
+ // srcSettings);
AlignFrame.this.setMenusForViewport();
}
});
{ src.getDbSource() }));
fetchr.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+
@Override
public void run()
{
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
+
@Override
public void finished()
{
fetchr.addActionListener(new ActionListener()
{
+
@Override
public void actionPerformed(ActionEvent e)
{
new Thread(new Runnable()
{
+
@Override
public void run()
{
dbRefFetcher
.addListener(new FetchFinishedListenerI()
{
+
@Override
public void finished()
{
/**
* Left justify the whole alignment.
*/
+
@Override
protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
/**
* Right justify the whole alignment.
*/
+
@Override
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
viewport.firePropertyChange("alignment", null, al);
}
+
@Override
public void setShowSeqFeatures(boolean b)
{
* jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
* awt.event.ActionEvent)
*/
+
@Override
protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
* .ActionEvent)
*/
+
@Override
protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
* .event.ActionEvent)
*/
+
@Override
protected void showGroupConservation_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
* .event.ActionEvent)
*/
+
@Override
protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
* .event.ActionEvent)
*/
+
@Override
protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+
@Override
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+
@Override
protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
* jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
* .event.ActionEvent)
*/
+
@Override
protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true, true);
+ alignPanel.paintAlignment(true,
+ viewport.needToUpdateStructureViews());
}
}
}
}
+
@Override
protected void createGroup_actionPerformed(ActionEvent e)
{
if (avc.createGroup())
{
+ if (applyAutoAnnotationSettings.isSelected())
+ {
+ alignPanel.updateAnnotation(true, false);
+ }
alignPanel.alignmentChanged();
}
}
+
@Override
protected void unGroup_actionPerformed(ActionEvent e)
{
* @param forAlignment
* update non-sequence-related annotations
*/
+
@Override
protected void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
/**
* Store selected annotation sort order for the view and repaint.
*/
+
@Override
protected void sortAnnotations_actionPerformed()
{
*/
public List<? extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ // alignPanels is never null
+ // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ return alignPanels;
}
/**
*
* @param show
*/
+
@Override
protected void showComplement_actionPerformed(boolean show)
{
* Generate the reverse (optionally complemented) of the selected sequences,
* and add them to the alignment
*/
+
@Override
protected void showReverse_actionPerformed(boolean complement)
{
* AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
* be targeted at this alignment.
*/
+
@Override
protected void runGroovy_actionPerformed()
{
} catch (Exception ex)
{
System.err.println((ex.toString()));
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.couldnt_run_groovy_script"),
MessageManager.getString("label.groovy_support_failed"),
JvOptionPane.ERROR_MESSAGE);
return false;
}
+
@Override
protected void selectHighlightedColumns_actionPerformed(
ActionEvent actionEvent)
colourMenu.add(textColour);
colourMenu.addSeparator();
- ColourMenuHelper.addMenuItems(colourMenu, this, viewport.getAlignment(),
- false);
+ ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
+ viewport.getAlignment(), false);
+ colourMenu.add(annotationColour);
+ bg.add(annotationColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(modifyConservation);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
}
}
+
@Override
protected void loadVcf_actionPerformed()
{
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
final AlignFrame us = this;
- chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+ 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);
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, us);
- }
+ }
+
+ private Rectangle lastFeatureSettingsBounds = null;
+
+
+ public void setFeatureSettingsGeometry(Rectangle bounds)
+ {
+ lastFeatureSettingsBounds = bounds;
+ }
+
+
+ public Rectangle getFeatureSettingsGeometry()
+ {
+ return lastFeatureSettingsBounds;
+ }
+
+
+ public void scrollTo(int row, int column)
+ {
+ alignPanel.getSeqPanel().scrollTo(row, column);
+ }
+
+
+ public void scrollToRow(int row)
+ {
+ alignPanel.getSeqPanel().scrollToRow(row);
+ }
+
+
+ public void scrollToColumn(int column)
+ {
+ alignPanel.getSeqPanel().scrollToColumn(column);
+ }
+
+ /**
+ * BH 2019 from JalviewLite
+ *
+ * get sequence feature groups that are hidden or shown
+ *
+ * @param visible
+ * true is visible
+ * @return list
+ */
+ public String[] getFeatureGroupsOfState(boolean visible)
+ {
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getGroups(visible);
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
- };
- }).openDialog(null);
+ /**
+ *
+ * @return list of feature groups on the view
+ */
+ public String[] getFeatureGroups()
+ {
+ jalview.api.FeatureRenderer fr = null;
+ if (alignPanel != null
+ && (fr = alignPanel.getFeatureRenderer()) != null)
+ {
+ List<String> gps = fr.getFeatureGroups();
+ String[] _gps = gps.toArray(new String[gps.size()]);
+ return _gps;
+ }
+ return null;
+ }
+ public void select(SequenceGroup sel, ColumnSelection csel,
+ HiddenColumns hidden)
+ {
+ alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
}
}
}
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff