X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=1f3f40992c7f3009a2a92385be270bbaa8691327;hb=490bea038483dcc853766de08a8971668930f43a;hp=7525f47cd350e5d40351178f6cc4a10460c7d348;hpb=ca5507100157d1727bf62ec39988ea540bbf88ec;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 7525f47..1f3f409 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,18 +20,72 @@ */ 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.Enumeration; +import java.util.Hashtable; +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.Dna; +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.api.AlignmentViewPanel; import jalview.api.FeatureSettingsControllerI; +import jalview.api.FeatureSettingsModelI; import jalview.api.SplitContainerI; import jalview.api.ViewStyleI; import jalview.api.analysis.SimilarityParamsI; @@ -45,7 +99,7 @@ import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; import jalview.commands.SlideSequencesCommand; import jalview.commands.TrimRegionCommand; -import jalview.datamodel.AlignExportSettingBeanI; +import jalview.datamodel.AlignExportSettingsAdapter; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -64,6 +118,7 @@ import jalview.gui.ColourMenuHelper.ColourChangeListener; 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; @@ -83,12 +138,14 @@ import jalview.io.ScoreMatrixFile; 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; @@ -98,68 +155,15 @@ import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.seqfetcher.DbSourceProxy; -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.beans.PropertyChangeListener; -import java.io.File; -import java.io.FileWriter; -import java.io.PrintWriter; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Deque; -import java.util.Enumeration; -import java.util.Hashtable; -import java.util.List; -import java.util.Vector; - -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.JTextPane; -import javax.swing.SwingUtilities; - /** * DOCUMENT ME! * * @author $author$ * @version $Revision$ */ +@SuppressWarnings("serial") public class AlignFrame extends GAlignFrame implements DropTargetListener, - IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener, - PropertyChangeListener + IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener { public static final int DEFAULT_WIDTH = 700; @@ -335,40 +339,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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() { +// setBackground(Color.white); // BH 2019 + if (!Jalview.isHeadlessMode()) { progressBar = new ProgressBar(this.statusPanel, this.statusBar); @@ -417,12 +395,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.desktop != null) { this.setDropTarget(new java.awt.dnd.DropTarget(this, this)); - /** - * BH 2018 ignore service listeners - * - * @j2sNative - * - */ + if (!Platform.isJS()) { addServiceListeners(); } @@ -441,7 +414,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addKeyListener(); - final List selviews = new ArrayList<>(); + final List selviews = new ArrayList<>(); final List origview = new ArrayList<>(); final String menuLabel = MessageManager .getString("label.copy_format_from"); @@ -653,7 +626,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_BACK_SPACE: if (!viewport.cursorMode) { - cut_actionPerformed(null); + cut_actionPerformed(); } else { @@ -705,7 +678,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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) @@ -791,9 +764,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } @@ -806,7 +779,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, expandViews.setEnabled(true); gatherViews.setEnabled(true); - tabbedPane.addTab(ap.av.viewName, ap); + tabbedPane.addTab(ap.av.getViewName(), ap); ap.setVisible(false); } @@ -829,7 +802,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } @@ -876,7 +849,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.removeJalviewPropertyChangeListener("services", thisListener); closeMenuItem_actionPerformed(true); - }; + } }); // Finally, build the menu once to get current service state new Thread(new Runnable() @@ -930,7 +903,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param av * AlignViewport */ - void setMenusFromViewport(AlignViewport av) + public void setMenusFromViewport(AlignViewport av) { padGapsMenuitem.setSelected(av.isPadGaps()); colourTextMenuItem.setSelected(av.isShowColourText()); @@ -1021,10 +994,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } /* @@ -1041,9 +1019,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void fetchSequence_actionPerformed(ActionEvent e) + public void fetchSequence_actionPerformed() { - new jalview.gui.SequenceFetcher(this); + new SequenceFetcher(this); } @Override @@ -1154,7 +1132,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (fileName == null || (currentFileFormat == null) || fileName.startsWith("http")) { - saveAs_actionPerformed(null); + saveAs_actionPerformed(); } else { @@ -1163,58 +1141,57 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * 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() + 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(); + value = chooser.showSaveDialog(this); + if (value != JalviewFileChooser.APPROVE_OPTION) { - 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); - } - - fileName = chooser.getSelectedFile().getPath(); + return; + } + } - Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat.getName()); + fileName = chooser.getSelectedFile().getPath(); - Cache.setProperty("LAST_DIRECTORY", fileName); - saveAlignment(fileName, currentFileFormat); - } - }).showSaveDialog(this); + Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName()); + Cache.setProperty("LAST_DIRECTORY", fileName); + saveAlignment(fileName, currentFileFormat); } - private boolean lastSaveSuccessful = false; + boolean lastSaveSuccessful = false; - private FileFormatI lastFormatSaved; + FileFormatI lastFormatSaved; - private String lastFilenameSaved; + String lastFilenameSaved; /** * Raise a dialog or status message for the last call to saveAlignment. @@ -1235,7 +1212,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { - statusBar.setText(MessageManager.formatMessage( + setStatus(MessageManager.formatMessage( "label.successfully_saved_to_file_in_format", new Object[] { lastFilenameSaved, lastFormatSaved })); @@ -1243,113 +1220,143 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return lastSaveSuccessful; } + /** + * 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) { - lastSaveSuccessful = false; + lastSaveSuccessful = true; lastFilenameSaved = file; lastFormatSaved = format; - AlignFrame us = this; + 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); } - - lastSaveSuccessful = 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() { - AlignExportSettingI settings = getAlignmentForExport(format, - alignPanel, null); - settings.addActionListener(new ActionListener() + @Override + public void run() { - @Override - public void actionPerformed(ActionEvent e) + lastSaveSuccessful = false; + } + }; + Runnable outputAction = new Runnable() + { + @Override + public void run() + { + // 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) { - - if (settings.isCancelled()) + lastSaveSuccessful = false; + } + else + { + // create backupfiles object and get new temp filename destination + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null; + try { - lastSaveSuccessful = false; - return; - } - AlignmentExportData exportData = settings.getAlignExportData(); - 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) + 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(); } - else + + if (doBackup) { - try - { - PrintWriter out = new PrintWriter(new FileWriter(file)); - - out.print(output); - out.close(); - us.setTitle(file); - statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", - new Object[] - { fileName, format.getName() })); - } catch (Exception ex) - { - lastSaveSuccessful = false; - ex.printStackTrace(); - } + backupfiles.setWriteSuccess(lastSaveSuccessful); + // do the backup file roll and rename the temp file to actual file + lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile(); } } - }); + } + }; - settings.doShowSettings(); + /* + * show dialog with export options if applicable; else just do it + */ + if (AlignExportOptions.isNeeded(viewport, format)) + { + AlignExportOptions choices = new AlignExportOptions( + alignPanel.getAlignViewport(), format, options); + choices.setResponseAction(0, outputAction); + choices.setResponseAction(1, cancelAction); + choices.showDialog(); + } + else + { + 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()); - AlignExportSettingI settings = getAlignmentForExport(fileFormat, - alignPanel, null); - settings.addActionListener(new ActionListener() + .forName(fileFormatName); + AlignExportSettingsI options = new AlignExportSettingsAdapter(false); + Runnable outputAction = new Runnable() { @Override - public void actionPerformed(ActionEvent e) + public void run() { - if (settings.isCancelled()) - { - return; - } - AlignmentExportData exportData = settings.getAlignExportData(); + // 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, settings) + cap.setText(new FormatAdapter(alignPanel, options) .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), exportData.getStartEndPostions(), @@ -1363,19 +1370,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, oom); cap.dispose(); } - // TODO Auto-generated method stub - } - }); - settings.doShowSettings(); - } - - public static AlignExportSettingI getAlignmentForExport( - FileFormatI format, AlignmentPanel alignPanel, - AlignExportSettingBeanI exportSettings) - { + }; - return new AlignExportSettings(alignPanel, format, exportSettings); + /* + * show dialog with export options if applicable; else just do it + */ + if (AlignExportOptions.isNeeded(viewport, fileFormat)) + { + AlignExportOptions choices = new AlignExportOptions( + alignPanel.getAlignViewport(), fileFormat, options); + choices.setResponseAction(0, outputAction); + choices.showDialog(); + } + else + { + outputAction.run(); + } } /** @@ -1404,33 +1415,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * 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 @@ -1472,13 +1489,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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")); - chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION) + String tooltip = MessageManager.getString("label.load_jalview_annotations"); + chooser.setDialogTitle(tooltip); + chooser.setToolTipText(tooltip); + chooser.setResponseHandler(0, new Runnable() { - @Override public void run() { @@ -1486,10 +1501,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); loadJalviewDataFile(chooser.getSelectedFile(), null, null, null); } - }); - chooser.openDialog(this); + chooser.showOpenDialog(this); } /** @@ -1528,9 +1542,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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 @@ -1764,10 +1782,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode * * @param up - * DOCUMENT ME! + * or down (if !up) */ public void moveSelectedSequences(boolean up) { @@ -1775,8 +1793,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (sg == null) { - return; + if (viewport.cursorMode) + { + sg = new SequenceGroup(); + sg.addSequence(viewport.getAlignment() + .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false); + } else { + return; + } } + + if (sg.getSize() < 1) + { + return; + } + + // TODO: JAL-3733 - add an event to the undo buffer for this ! + viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true, false); @@ -1894,7 +1927,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void copy_actionPerformed(ActionEvent e) + protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) { @@ -1946,7 +1979,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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() })); } @@ -2069,7 +2102,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, && 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 newDs = (importDs) ? new Vector<>() : null; // used to + // create // minimum dataset set for (int i = 0; i < sequences.length; i++) @@ -2142,7 +2176,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, - new Integer(++fgroup)); + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2189,7 +2223,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newGraphGroups.add(q, null); } newGraphGroups.set(newann.graphGroup, - new Integer(++fgroup)); + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2208,7 +2242,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - viewport.getRanges().setEndSeq(alignment.getHeight()); + viewport.getRanges().setEndSeq(alignment.getHeight() - 1); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2363,26 +2397,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * 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(); @@ -2391,52 +2419,56 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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(); + } } /** @@ -2465,15 +2497,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @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); - } + 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 @@ -2498,7 +2527,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); - viewport.setSelectionGroup(null); + viewport.setSearchResults(null); alignPanel.getIdPanel().getIdCanvas().searchResults = null; // JAL-2034 - should delegate to // alignPanel to decide if overview needs @@ -2611,7 +2640,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, column, viewport.getAlignment()); } - statusBar.setText(MessageManager + setStatus(MessageManager .formatMessage("label.removed_columns", new String[] { Integer.valueOf(trimRegion.getSize()).toString() })); @@ -2661,7 +2690,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); - statusBar.setText(MessageManager + setStatus(MessageManager .formatMessage("label.removed_empty_columns", new Object[] { Integer.valueOf(removeGapCols.getSize()).toString() })); @@ -2735,15 +2764,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Opens a Finder dialog * * @param e - * DOCUMENT ME! */ @Override public void findMenuItem_actionPerformed(ActionEvent e) { - new Finder(); + new Finder(alignPanel); } /** @@ -2769,7 +2797,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * 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) { /* @@ -2781,10 +2810,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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")); } /* @@ -2794,6 +2823,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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 @@ -2808,7 +2843,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.refresh(true); // adjust layout of annotations } - newap.av.viewName = getNewViewName(viewTitle); + newap.av.setViewName(getNewViewName(viewTitle)); addAlignmentPanel(newap, true); newap.alignmentChanged(); @@ -2871,9 +2906,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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()); } } } @@ -2956,7 +2991,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setFollowHighlight(state); if (state) { - alignPanel.scrollToPosition(viewport.getSearchResults(), false); + alignPanel.scrollToPosition(viewport.getSearchResults()); } } @@ -3015,7 +3050,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param toggleSeqs * @param toggleCols */ - private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) + protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols) { boolean hide = false; @@ -3103,6 +3138,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3127,6 +3163,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3148,7 +3185,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } @@ -3162,6 +3199,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3175,6 +3213,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); + alignPanel.updateLayout(); alignPanel.paintAlignment(true, false); } @@ -3228,9 +3267,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void featureSettings_actionPerformed(ActionEvent e) { + showFeatureSettingsUI(); + } + + @Override + public FeatureSettingsControllerI showFeatureSettingsUI() + { if (featureSettings != null) { - featureSettings.close(); + featureSettings.closeOldSettings(); featureSettings = null; } if (!showSeqFeatures.isSelected()) @@ -3240,6 +3285,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSeqFeatures_actionPerformed(null); } featureSettings = new FeatureSettings(this); + return featureSettings; } /** @@ -3288,8 +3334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { contents.toString() }); contents = null; - if (/** @j2sNative true || */ - false) + if (Platform.isJS()) { JLabel textLabel = new JLabel(); textLabel.setText(content); @@ -3297,9 +3342,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, pane = new JPanel(new BorderLayout()); ((JPanel) pane).setOpaque(true); - ((JPanel) pane).add(textLabel, BorderLayout.CENTER); + pane.setBackground(Color.WHITE); + ((JPanel) pane).add(textLabel, BorderLayout.NORTH); } else + /** + * Java only + * + * @j2sIgnore + */ { JEditorPane editPane = new JEditorPane("text/html", ""); editPane.setEditable(false); @@ -3348,7 +3399,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { overview.dispose(); alignPanel.setOverviewPanel(null); - }; + } }); if (getKeyListeners().length > 0) { @@ -3418,6 +3469,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * otherwise set the chosen colour scheme (or null for 'None') */ ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name, + viewport, viewport.getAlignment(), viewport.getHiddenRepSequences()); changeColour(cs); } @@ -3687,9 +3739,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frameTitle += " from "; - if (viewport.viewName != null) + if (viewport.getViewName() != null) { - frameTitle += viewport.viewName + " of "; + frameTitle += viewport.getViewName() + " of "; } frameTitle += this.title; @@ -3785,7 +3837,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { sortByAnnotScore.removeAll(); // almost certainly a quicker way to do this - but we keep it simple - Hashtable scoreSorts = new Hashtable(); + Hashtable scoreSorts = new Hashtable<>(); AlignmentAnnotation aann[]; for (SequenceI sqa : viewport.getAlignment().getSequences()) { @@ -3798,11 +3850,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } } - Enumeration labels = scoreSorts.keys(); + Enumeration labels = scoreSorts.keys(); while (labels.hasMoreElements()) { addSortByAnnotScoreMenuItem(sortByAnnotScore, - (String) labels.nextElement()); + labels.nextElement()); } sortByAnnotScore.setVisible(scoreSorts.size() > 0); scoreSorts.clear(); @@ -3969,8 +4021,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, chooser.setToolTipText( MessageManager.getString("label.load_tree_file")); - chooser.response(new jalview.util.dialogrunner.RunResponse( - JalviewFileChooser.APPROVE_OPTION) + chooser.setResponseHandler(0,new Runnable() { @Override public void run() @@ -4000,7 +4051,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JvOptionPane.WARNING_MESSAGE); } } - }).openDialog(this); + }); + chooser.showOpenDialog(this); } public TreePanel showNewickTree(NewickFile nf, String treeTitle) @@ -4130,14 +4182,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // No MSAWS used any more: // Vector msaws = null; // (Vector) // Discoverer.services.get("MsaWS"); - Vector secstrpr = (Vector) Discoverer.services + Vector 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); @@ -4247,7 +4299,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @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 @@ -4355,14 +4407,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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( @@ -4391,7 +4443,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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)) { @@ -4516,8 +4568,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, : 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) @@ -4591,13 +4648,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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++; } @@ -4697,7 +4754,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, changeColour( new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; - statusBar.setText(MessageManager.getString( + setStatus(MessageManager.getString( "label.successfully_pasted_tcoffee_scores_to_alignment")); } else @@ -4740,7 +4797,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new FileParse(file, sourceType)); sm.parse(); // todo: i18n this message - statusBar.setText(MessageManager.formatMessage( + setStatus(MessageManager.formatMessage( "label.successfully_loaded_matrix", sm.getMatrixName())); } @@ -4758,7 +4815,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (parseFeaturesFile(file, sourceType)) { - alignPanel.paintAlignment(true, true); + SplitFrame splitFrame = (SplitFrame) getSplitViewContainer(); + if (splitFrame != null) + { + splitFrame.repaint(); + } + else + { + alignPanel.paintAlignment(true, true); + } } } else @@ -4814,6 +4879,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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(); + } + } + } /* @@ -4866,12 +4946,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); } @@ -4982,7 +5062,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, trimrs.setSelected(trimrs.isSelected()); Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); - }; + } }); rfetch.add(trimrs); JMenuItem fetchr = new JMenuItem( @@ -5011,6 +5091,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void finished() { + + for (FeatureSettingsModelI srcSettings : dbRefFetcher + .getFeatureSettingsModels()) + { + + alignPanel.av.mergeFeaturesStyle(srcSettings); + } AlignFrame.this.setMenusForViewport(); } }); @@ -5022,22 +5109,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); 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 otherdb; JMenu dfetch = new JMenu(); JMenu ifetch = new JMenu(); @@ -5054,12 +5138,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { continue; } - // List dbs=otherdb; - // otherdb=new ArrayList(); - // for (DbSourceProxy db:dbs) - // { - // if (!db.isA(DBRefSource.ALIGNMENTDB) - // } if (mname == null) { mname = "From " + dbclass; @@ -5096,6 +5174,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void finished() { + FeatureSettingsModelI srcSettings = dassource[0] + .getFeatureColourScheme(); + alignPanel.av.mergeFeaturesStyle( + srcSettings); AlignFrame.this.setMenusForViewport(); } }); @@ -5388,7 +5470,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true, true); + alignPanel.paintAlignment(true, + viewport.needToUpdateStructureViews()); } } @@ -5409,6 +5492,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (avc.createGroup()) { + if (applyAutoAnnotationSettings.isSelected()) + { + alignPanel.updateAnnotation(true, false); + } alignPanel.alignmentChanged(); } } @@ -5499,7 +5586,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public List getAlignPanels() { - return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + // alignPanels is never null + // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels; + return alignPanels; } /** @@ -5668,15 +5757,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); @@ -5703,24 +5793,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); - } - - }; - }).openDialog(null); + } + private Rectangle lastFeatureSettingsBounds = null; + @Override + public void setFeatureSettingsGeometry(Rectangle bounds) + { + lastFeatureSettingsBounds = bounds; } + @Override + public Rectangle getFeatureSettingsGeometry() + { + return lastFeatureSettingsBounds; + } } class PrintThread extends Thread