X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=5e16397a17ee1d3f906698682e7084395260f62d;hb=af259f508805faf2da90585ee9a67cd7853bf5aa;hp=e5d550f7a597f7ad201297c652c71ca240629b06;hpb=c4b90e7ff57436d6bb96d316eed24c887b241f4d;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index e5d550f..5e16397 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -20,10 +20,59 @@ */ package jalview.gui; +import java.awt.BorderLayout; +import java.awt.Component; +import java.awt.Rectangle; +import java.awt.Toolkit; +import java.awt.datatransfer.Clipboard; +import java.awt.datatransfer.DataFlavor; +import java.awt.datatransfer.StringSelection; +import java.awt.datatransfer.Transferable; +import java.awt.dnd.DnDConstants; +import java.awt.dnd.DropTargetDragEvent; +import java.awt.dnd.DropTargetDropEvent; +import java.awt.dnd.DropTargetEvent; +import java.awt.dnd.DropTargetListener; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusAdapter; +import java.awt.event.FocusEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyAdapter; +import java.awt.event.KeyEvent; +import java.awt.event.MouseEvent; +import java.awt.print.PageFormat; +import java.awt.print.PrinterJob; +import java.beans.PropertyChangeEvent; +import java.io.File; +import java.io.FileWriter; +import java.io.IOException; +import java.io.PrintWriter; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Deque; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JEditorPane; +import javax.swing.JInternalFrame; +import javax.swing.JLayeredPane; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JScrollPane; +import javax.swing.SwingUtilities; + 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; @@ -32,6 +81,7 @@ 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; @@ -64,6 +114,7 @@ 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; @@ -81,12 +132,14 @@ import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; import jalview.io.ScoreMatrixFile; import jalview.io.TCoffeeScoreFile; +import jalview.io.vcf.VCFLoader; import jalview.jbgui.GAlignFrame; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; @@ -96,52 +149,6 @@ import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.seqfetcher.DbSourceProxy; -import java.awt.BorderLayout; -import java.awt.Component; -import java.awt.Rectangle; -import java.awt.Toolkit; -import java.awt.datatransfer.Clipboard; -import java.awt.datatransfer.DataFlavor; -import java.awt.datatransfer.StringSelection; -import java.awt.datatransfer.Transferable; -import java.awt.dnd.DnDConstants; -import java.awt.dnd.DropTargetDragEvent; -import java.awt.dnd.DropTargetDropEvent; -import java.awt.dnd.DropTargetEvent; -import java.awt.dnd.DropTargetListener; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.FocusAdapter; -import java.awt.event.FocusEvent; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyAdapter; -import java.awt.event.KeyEvent; -import java.awt.event.MouseEvent; -import java.awt.print.PageFormat; -import java.awt.print.PrinterJob; -import java.beans.PropertyChangeEvent; -import java.io.File; -import java.io.FileWriter; -import java.io.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.JEditorPane; -import javax.swing.JInternalFrame; -import javax.swing.JLayeredPane; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JScrollPane; -import javax.swing.SwingUtilities; - /** * DOCUMENT ME! * @@ -163,8 +170,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; - ViewportRanges vpRanges; - public AlignViewControllerI avc; List alignPanels = new ArrayList<>(); @@ -234,8 +239,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param height * height of frame. */ - public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, - int width, int height) + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height) { this(al, hiddenColumns, width, height, null); } @@ -251,8 +256,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param sequenceSetId * (may be null) */ - public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, - int width, int height, String sequenceSetId) + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height, String sequenceSetId) { this(al, hiddenColumns, width, height, sequenceSetId, null); } @@ -270,8 +275,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param viewId * (may be null) */ - public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, - int width, int height, String sequenceSetId, String viewId) + public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width, + int height, String sequenceSetId, String viewId) { setSize(width, height); @@ -336,7 +341,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, progressBar = new ProgressBar(this.statusPanel, this.statusBar); } - vpRanges = viewport.getRanges(); avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) @@ -510,9 +514,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void keyPressed(KeyEvent evt) { if (viewport.cursorMode - && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt - .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt - .getKeyCode() <= KeyEvent.VK_NUMPAD9)) + && ((evt.getKeyCode() >= KeyEvent.VK_0 + && evt.getKeyCode() <= KeyEvent.VK_9) + || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 + && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)) && Character.isDigit(evt.getKeyChar())) { alignPanel.getSeqPanel().numberPressed(evt.getKeyChar()); @@ -533,7 +538,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, 1); + alignPanel.getSeqPanel().moveCursor(0, 1, + evt.isShiftDown() && !evt.isAltDown()); } break; @@ -544,19 +550,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (viewport.cursorMode) { - alignPanel.getSeqPanel().moveCursor(0, -1); + alignPanel.getSeqPanel().moveCursor(0, -1, + evt.isShiftDown() && !evt.isAltDown()); } - break; case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { - slideSequences(false, alignPanel.getSeqPanel().getKeyboardNo1()); + slideSequences(false, + alignPanel.getSeqPanel().getKeyboardNo1()); } else { - alignPanel.getSeqPanel().moveCursor(-1, 0); + alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown()); } break; @@ -568,16 +575,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().moveCursor(1, 0); + alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown()); } break; case KeyEvent.VK_SPACE: if (viewport.cursorMode) { - alignPanel.getSeqPanel().insertGapAtCursor( - evt.isControlDown() || evt.isShiftDown() - || evt.isAltDown()); + alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); } break; @@ -600,9 +606,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - alignPanel.getSeqPanel().deleteGapAtCursor( - evt.isControlDown() || evt.isShiftDown() - || evt.isAltDown()); + alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() || evt.isAltDown()); } break; @@ -649,14 +654,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; - statusBar.setText(MessageManager.formatMessage( - "label.keyboard_editing_mode", - new String[] { (viewport.cursorMode ? "on" : "off") })); + statusBar.setText(MessageManager + .formatMessage("label.keyboard_editing_mode", new String[] + { (viewport.cursorMode ? "on" : "off") })); if (viewport.cursorMode) { - alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges + ViewportRanges ranges = viewport.getRanges(); + alignPanel.getSeqPanel().seqCanvas.cursorX = ranges .getStartRes(); - alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges + alignPanel.getSeqPanel().seqCanvas.cursorY = ranges .getStartSeq(); } alignPanel.getSeqPanel().seqCanvas.repaint(); @@ -689,10 +695,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, break; } case KeyEvent.VK_PAGE_UP: - vpRanges.pageUp(); + viewport.getRanges().pageUp(); break; case KeyEvent.VK_PAGE_DOWN: - vpRanges.pageDown(); + viewport.getRanges().pageDown(); break; } } @@ -705,16 +711,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_LEFT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } break; case KeyEvent.VK_RIGHT: if (evt.isAltDown() || !viewport.cursorMode) { - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } break; } @@ -734,9 +740,9 @@ 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); } @@ -749,7 +755,7 @@ 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); } @@ -772,7 +778,7 @@ 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); } @@ -800,8 +806,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { - System.err - .println("Rebuild WS Menu for service change"); + System.err.println( + "Rebuild WS Menu for service change"); BuildWebServiceMenu(); } @@ -841,17 +847,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentI al = getViewport().getAlignment(); boolean nucleotide = al.isNucleotide(); + loadVcf.setVisible(nucleotide); showTranslation.setVisible(nucleotide); showReverse.setVisible(nucleotide); showReverseComplement.setVisible(nucleotide); conservationMenuItem.setEnabled(!nucleotide); - modifyConservation.setEnabled(!nucleotide - && conservationMenuItem.isSelected()); + modifyConservation + .setEnabled(!nucleotide && conservationMenuItem.isSelected()); showGroupConservation.setEnabled(!nucleotide); - showComplementMenuItem.setText(nucleotide ? MessageManager - .getString("label.protein") : MessageManager - .getString("label.nucleotide")); + showComplementMenuItem + .setText(nucleotide ? MessageManager.getString("label.protein") + : MessageManager.getString("label.nucleotide")); } /** @@ -872,7 +879,7 @@ 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()); @@ -963,10 +970,15 @@ 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); } /* @@ -1025,7 +1037,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.closeAssociatedWindows(); FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL + DataSourceType protocol = fileName.startsWith("http:") + ? DataSourceType.URL : DataSourceType.FILE; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } @@ -1034,7 +1047,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL + DataSourceType protocol = fileName.startsWith("http:") + ? DataSourceType.URL : DataSourceType.FILE; AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); @@ -1066,8 +1080,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void addFromText_actionPerformed(ActionEvent e) { - Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport - .getAlignPanel()); + Desktop.instance + .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel()); } @Override @@ -1099,14 +1113,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void saveAs_actionPerformed(ActionEvent e) { - String format = currentFileFormat == null ? null : currentFileFormat - .getName(); - JalviewFileChooser chooser = JalviewFileChooser.forWrite( - Cache.getProperty("LAST_DIRECTORY"), format); + String format = currentFileFormat == null ? null + : currentFileFormat.getName(); + JalviewFileChooser chooser = JalviewFileChooser + .forWrite(Cache.getProperty("LAST_DIRECTORY"), format); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.save_alignment_to_file")); + chooser.setDialogTitle( + MessageManager.getString("label.save_alignment_to_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -1116,14 +1130,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); + 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) @@ -1151,15 +1162,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (shortName.indexOf(java.io.File.separatorChar) > -1) { - shortName = shortName.substring(shortName - .lastIndexOf(java.io.File.separatorChar) + 1); + shortName = shortName.substring( + shortName.lastIndexOf(java.io.File.separatorChar) + 1); } - success = new Jalview2XML().saveAlignment(this, file, shortName); + success = new jalview.project.Jalview2XML().saveAlignment(this, file, + shortName); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] { - fileName, format })); + "label.successfully_saved_to_file_in_format", new Object[] + { file, format })); } else @@ -1172,13 +1184,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } FormatAdapter f = new FormatAdapter(alignPanel, exportData.getSettings()); - String output = f.formatSequences( - format, - exportData.getAlignment(), // class cast exceptions will + 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()); + f.getCacheSuffixDefault(format), + viewport.getAlignment().getHiddenColumns()); if (output == null) { @@ -1186,31 +1199,67 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { + // create backupfiles object and get new temp filename destination + Cache.log.trace("ALIGNFRAME making backupfiles object for " + file); + BackupFiles backupfiles = new BackupFiles(file); + try { - PrintWriter out = new PrintWriter(new FileWriter(file)); + String tempFilePath = backupfiles.getTempFilePath(); + Cache.log.trace( + "ALIGNFRAME setting PrintWriter to " + tempFilePath); + PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + + Cache.log.trace( + "ALIGNFRAME about to write to temp file " + tempFilePath); out.print(output); + Cache.log.trace("ALIGNFRAME about to close file"); out.close(); + Cache.log.trace("ALIGNFRAME closed file"); this.setTitle(file); statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", - new Object[] { fileName, format.getName() })); + "label.successfully_saved_to_file_in_format", new Object[] + { file, format.getName() })); + } catch (IOException e) + { + success = false; + Cache.log.error( + "ALIGNFRAME Something happened writing the temp file"); + Cache.log.error(e.getMessage()); + Cache.log.debug(Cache.getStackTraceString(e)); + } catch (Exception ex) { success = false; - ex.printStackTrace(); + Cache.log.error( + "ALIGNFRAME Something unexpected happened writing the temp file"); + Cache.log.error(ex.getMessage()); + Cache.log.debug(Cache.getStackTraceString(ex)); } + + backupfiles.setWriteSuccess(success); + Cache.log.debug("ALIGNFRAME writing temp file was " + + (success ? "" : "NOT ") + "successful"); + // do the backup file roll and rename the temp file to actual file + Cache.log.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile"); + success = backupfiles.rollBackupsAndRenameTempFile(); + Cache.log.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile " + + (success ? "" : "un") + "successfully"); + } } if (!success) { - JvOptionPane.showInternalMessageDialog(this, MessageManager - .formatMessage("label.couldnt_save_file", - new Object[] { fileName }), MessageManager - .getString("label.error_saving_file"), - JvOptionPane.WARNING_MESSAGE); + if (!Platform.isHeadless()) + { + JvOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_save_file", new Object[] + { file }), + MessageManager.getString("label.error_saving_file"), + JvOptionPane.WARNING_MESSAGE); + } } return success; @@ -1240,8 +1289,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void outputText_actionPerformed(ActionEvent e) { - FileFormatI fileFormat = FileFormats.getInstance().forName( - e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance() + .forName(e.getActionCommand()); AlignmentExportData exportData = getAlignmentForExport(fileFormat, viewport, null); if (exportData.getSettings().isCancelled()) @@ -1256,15 +1305,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); + exportData.getStartEndPostions(), + viewport.getAlignment().getHiddenColumns())); + Desktop.addInternalFrame(cap, MessageManager + .formatMessage("label.alignment_output_command", new Object[] + { e.getActionCommand() }), 600, 500); } catch (OutOfMemoryError oom) { - new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); + new OOMWarning("Outputting alignment as " + e.getActionCommand(), + oom); cap.dispose(); } @@ -1392,13 +1441,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void exportFeatures_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportFeatures(alignPanel); + new AnnotationExporter(alignPanel).exportFeatures(); } @Override public void exportAnnotations_actionPerformed(ActionEvent e) { - new AnnotationExporter().exportAnnotations(alignPanel); + new AnnotationExporter(alignPanel).exportAnnotations(); } @Override @@ -1408,10 +1457,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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.setDialogTitle( + MessageManager.getString("label.load_jalview_annotations")); + chooser.setToolTipText( + MessageManager.getString("label.load_jalview_annotations")); int value = chooser.showOpenDialog(null); @@ -1460,9 +1509,13 @@ 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 @@ -1510,9 +1563,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { undoMenuItem.setEnabled(true); CommandI command = viewport.getHistoryList().peek(); - undoMenuItem.setText(MessageManager.formatMessage( - "label.undo_command", - new Object[] { command.getDescription() })); + undoMenuItem.setText(MessageManager + .formatMessage("label.undo_command", new Object[] + { command.getDescription() })); } else { @@ -1525,9 +1578,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, redoMenuItem.setEnabled(true); CommandI command = viewport.getRedoList().peek(); - redoMenuItem.setText(MessageManager.formatMessage( - "label.redo_command", - new Object[] { command.getDescription() })); + redoMenuItem.setText(MessageManager + .formatMessage("label.redo_command", new Object[] + { command.getDescription() })); } else { @@ -1599,8 +1652,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (originalSource != viewport) { - Cache.log - .warn("Implementation worry: mismatch of viewport origin for undo"); + Cache.log.warn( + "Implementation worry: mismatch of viewport origin for undo"); } originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != @@ -1608,8 +1661,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, originalSource - .getAlignment().getSequences()); + originalSource.firePropertyChange("alignment", null, + originalSource.getAlignment().getSequences()); } } @@ -1639,8 +1692,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (originalSource != viewport) { - Cache.log - .warn("Implementation worry: mismatch of viewport origin for redo"); + Cache.log.warn( + "Implementation worry: mismatch of viewport origin for redo"); } originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns = (viewport.getColumnSelection() != @@ -1648,8 +1701,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // && viewport.getColumnSelection().getHiddenColumns() != null && // viewport.getColumnSelection() // .getHiddenColumns().size() > 0); - originalSource.firePropertyChange("alignment", null, originalSource - .getAlignment().getSequences()); + originalSource.firePropertyChange("alignment", null, + originalSource.getAlignment().getSequences()); } } @@ -1664,8 +1717,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { EditCommand editCommand = (EditCommand) command; al = editCommand.getAlignment(); - List comps = PaintRefresher.components.get(viewport - .getSequenceSetId()); + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); for (Component comp : comps) { @@ -1711,23 +1764,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } synchronized void slideSequences(boolean right, int size) { List sg = new ArrayList<>(); - if (viewport.cursorMode) + if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup() + .getSize() != viewport.getAlignment().getHeight()) { - sg.add(viewport.getAlignment().getSequenceAt( - alignPanel.getSeqPanel().seqCanvas.cursorY)); + sg = viewport.getSelectionGroup() + .getSequences(viewport.getHiddenRepSequences()); } - else if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().getSize() != viewport - .getAlignment().getHeight()) + + if (sg.size() == 0 && viewport.cursorMode) { - sg = viewport.getSelectionGroup().getSequences( - viewport.getHiddenRepSequences()); + sg.add(viewport.getAlignment() + .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY)); } if (sg.size() < 1) @@ -1756,13 +1809,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SlideSequencesCommand ssc; if (right) { - ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, - size, viewport.getGapCharacter()); + ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size, + viewport.getGapCharacter()); } else { - ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, - size, viewport.getGapCharacter()); + ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size, + viewport.getGapCharacter()); } int groupAdjustment = 0; @@ -1807,9 +1860,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!inSplitFrame && historyList != null && historyList.size() > 0 && historyList.peek() instanceof SlideSequencesCommand) { - appendHistoryItem = ssc - .appendSlideCommand((SlideSequencesCommand) historyList - .peek()); + appendHistoryItem = ssc.appendSlideCommand( + (SlideSequencesCommand) historyList.peek()); } if (!appendHistoryItem) @@ -1829,7 +1881,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void copy_actionPerformed(ActionEvent e) { - System.gc(); if (viewport.getSelectionGroup() == null) { return; @@ -1857,37 +1908,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(""), null); - Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(ss, Desktop.instance); + Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss, + Desktop.instance); } catch (OutOfMemoryError er) { new OOMWarning("copying region", er); return; } - ArrayList hiddenColumns = null; + HiddenColumns hiddenColumns = null; if (viewport.hasHiddenColumns()) { - hiddenColumns = new ArrayList<>(); int hiddenOffset = viewport.getSelectionGroup().getStartRes(); int hiddenCutoff = viewport.getSelectionGroup().getEndRes(); - ArrayList hiddenRegions = viewport.getAlignment() - .getHiddenColumns().getHiddenColumnsCopy(); - for (int[] region : hiddenRegions) - { - if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff) - { - hiddenColumns.add(new int[] { region[0] - hiddenOffset, - region[1] - hiddenOffset }); - } - } + + // create new HiddenColumns object with copy of hidden regions + // between startRes and endRes, offset by startRes + hiddenColumns = new HiddenColumns( + viewport.getAlignment().getHiddenColumns(), hiddenOffset, + hiddenCutoff, hiddenOffset); } Desktop.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; statusBar.setText(MessageManager.formatMessage( - "label.copied_sequences_to_clipboard", new Object[] { Integer - .valueOf(seqs.length).toString() })); + "label.copied_sequences_to_clipboard", new Object[] + { Integer.valueOf(seqs.length).toString() })); } /** @@ -2037,8 +2083,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // copy and derive new dataset sequence sequences[i] = sequences[i].deriveSequence(); - alignment.getDataset().addSequence( - sequences[i].getDatasetSequence()); + alignment.getDataset() + .addSequence(sequences[i].getDatasetSequence()); // TODO: avoid creation of duplicate dataset sequences with a // 'contains' method using SequenceI.equals()/SequenceI.contains() } @@ -2068,18 +2114,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, annotationAdded = true; if (alann[i].sequenceRef == null && !alann[i].autoCalculated) { - AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]); + AlignmentAnnotation newann = new AlignmentAnnotation( + alann[i]); if (newann.graphGroup > -1) { if (newGraphGroups.size() <= newann.graphGroup || newGraphGroups.get(newann.graphGroup) == null) { - for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++) + for (int q = newGraphGroups + .size(); q <= newann.graphGroup; q++) { newGraphGroups.add(q, null); } - newGraphGroups.set(newann.graphGroup, new Integer( - ++fgroup)); + newGraphGroups.set(newann.graphGroup, + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2098,7 +2146,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // addHistoryItem(new EditCommand( MessageManager.getString("label.add_sequences"), - Action.PASTE, sequences, 0, alignment.getWidth(), alignment)); + Action.PASTE, sequences, 0, alignment.getWidth(), + alignment)); } // Add any annotations attached to sequences for (int i = 0; i < sequences.length; i++) @@ -2119,12 +2168,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (newGraphGroups.size() <= newann.graphGroup || newGraphGroups.get(newann.graphGroup) == null) { - for (int q = newGraphGroups.size(); q <= newann.graphGroup; q++) + for (int q = newGraphGroups + .size(); q <= newann.graphGroup; q++) { newGraphGroups.add(q, null); } - newGraphGroups.set(newann.graphGroup, new Integer( - ++fgroup)); + newGraphGroups.set(newann.graphGroup, + Integer.valueOf(++fgroup)); } newann.graphGroup = newGraphGroups.get(newann.graphGroup) .intValue(); @@ -2134,8 +2184,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // was // duplicated // earlier - alignment - .setAnnotationIndex(sequences[i].getAnnotation()[a], a); + alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], + a); } } } @@ -2143,7 +2193,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // propagate alignment changed. - vpRanges.setEndSeq(alignment.getHeight()); + viewport.getRanges().setEndSeq(alignment.getHeight()); if (annotationAdded) { // Duplicate sequence annotation in all views. @@ -2205,19 +2255,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int[] region : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is // found!!<<< af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings( - alignPanel.getSeqPanel().seqCanvas - .getFeatureRenderer()); + .transferSettings(alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2256,8 +2302,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { try { - AlignmentI alignment = AlignmentUtils.expandContext(getViewport() - .getAlignment(), -1); + AlignmentI alignment = AlignmentUtils + .expandContext(getViewport().getAlignment(), -1); AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, DEFAULT_HEIGHT); String newtitle = new String("Flanking alignment"); @@ -2265,19 +2311,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (Desktop.jalviewClipboard != null && Desktop.jalviewClipboard[2] != null) { - List hc = (List) Desktop.jalviewClipboard[2]; - for (int region[] : hc) - { - af.viewport.hideColumns(region[0], region[1]); - } + HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2]; + af.viewport.setHiddenColumns(hc); } // >>>This is a fix for the moment, until a better solution is // found!!<<< af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings( - alignPanel.getSeqPanel().seqCanvas - .getFeatureRenderer()); + .transferSettings(alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer()); // TODO: maintain provenance of an alignment, rather than just make the // title a concatenation of operations. @@ -2339,8 +2381,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ if (sg.getSize() == viewport.getAlignment().getHeight()) { - boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport - .getAlignment().getWidth()) ? true : false; + boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + + 1) == viewport.getAlignment().getWidth()) ? true : false; if (isEntireAlignWidth) { int confirm = JvOptionPane.showConfirmDialog(this, @@ -2369,8 +2411,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.sendSelection(); viewport.getAlignment().deleteGroup(sg); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); if (viewport.getAlignment().getHeight() < 1) { try @@ -2395,7 +2437,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -2408,20 +2450,17 @@ 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 // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); } @@ -2441,12 +2480,12 @@ 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 // updating. - alignPanel.paintAlignment(false); + alignPanel.paintAlignment(false, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2477,7 +2516,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // alignPanel to decide if overview needs // updating. - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId()); viewport.sendSelection(); } @@ -2486,7 +2525,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); viewport.sendSelection(); } @@ -2533,8 +2572,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.getHiddenRepSequences()); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); } else { @@ -2546,7 +2585,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { trimRegion = new TrimRegionCommand("Remove Left", true, seqs, column, viewport.getAlignment()); - vpRanges.setStartRes(0); + viewport.getRanges().setStartRes(0); } else { @@ -2554,10 +2593,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, column, viewport.getAlignment()); } - statusBar.setText(MessageManager.formatMessage( - "label.removed_columns", - new String[] { Integer.valueOf(trimRegion.getSize()) - .toString() })); + statusBar.setText(MessageManager + .formatMessage("label.removed_columns", new String[] + { Integer.valueOf(trimRegion.getSize()).toString() })); addHistoryItem(trimRegion); @@ -2570,8 +2608,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } } @@ -2589,8 +2627,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.getHiddenRepSequences()); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -2605,23 +2643,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); - statusBar.setText(MessageManager.formatMessage( - "label.removed_empty_columns", - new Object[] { Integer.valueOf(removeGapCols.getSize()) - .toString() })); + statusBar.setText(MessageManager + .formatMessage("label.removed_empty_columns", new Object[] + { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(vpRanges.getStartRes()); + ViewportRanges ranges = viewport.getRanges(); + int startRes = seq.findPosition(ranges.getStartRes()); // ShiftList shifts; // viewport.getAlignment().removeGaps(shifts=new ShiftList()); // edit.alColumnChanges=shifts.getInverse(); // if (viewport.hasHiddenColumns) // viewport.getColumnSelection().compensateForEdits(shifts); - vpRanges.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + ranges.setStartRes(seq.findIndex(startRes) - 1); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } @@ -2639,8 +2677,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray( - viewport.getHiddenRepSequences()); + seqs = viewport.getSelectionGroup() + .getSequencesAsArray(viewport.getHiddenRepSequences()); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } @@ -2652,15 +2690,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // This is to maintain viewport position on first residue // of first sequence SequenceI seq = viewport.getAlignment().getSequenceAt(0); - int startRes = seq.findPosition(vpRanges.getStartRes()); + int startRes = seq.findPosition(viewport.getRanges().getStartRes()); addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end, viewport.getAlignment())); - vpRanges.setStartRes(seq.findIndex(startRes) - 1); + viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } @@ -2674,20 +2712,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.setPadGaps(padGapsMenuitem.isSelected()); - viewport.firePropertyChange("alignment", null, viewport.getAlignment() - .getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } /** - * DOCUMENT ME! + * Opens a Finder dialog * * @param e - * DOCUMENT ME! */ @Override public void findMenuItem_actionPerformed(ActionEvent e) { - new Finder(); + new Finder(alignPanel); } /** @@ -2713,8 +2750,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * Create a new AlignmentPanel (with its own, new Viewport) */ - AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel, - true); + AlignmentPanel newap = new jalview.project.Jalview2XML() + .copyAlignPanel(alignPanel); if (!copyAnnotation) { /* @@ -2726,10 +2763,10 @@ 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")); } /* @@ -2739,6 +2776,12 @@ 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 @@ -2753,7 +2796,7 @@ 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(); @@ -2789,8 +2832,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } String newViewName = viewTitle + ((addFirstIndex) ? " " + index : ""); - List comps = PaintRefresher.components.get(viewport - .getSequenceSetId()); + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); List existingNames = getExistingViewNames(comps); @@ -2816,9 +2859,9 @@ 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()); } } } @@ -2868,21 +2911,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.getIdPanel().getIdCanvas() .setPreferredSize(alignPanel.calculateIdWidth()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } @Override public void idRightAlign_actionPerformed(ActionEvent e) { viewport.setRightAlignIds(idRightAlign.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /* @@ -2901,7 +2944,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setFollowHighlight(state); if (state) { - alignPanel.scrollToPosition(viewport.getSearchResults(), false); + alignPanel.scrollToPosition(viewport.getSearchResults()); } } @@ -2915,7 +2958,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -2944,7 +2987,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); - repaint(); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -2952,7 +2995,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); - // alignPanel.paintAlignment(true); } /** @@ -2971,9 +3013,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Hide everything by the current selection - this is a hack - we do the // invert and then hide // first check that there will be visible columns after the invert. - if (viewport.hasSelectedColumns() - || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg - .getEndRes())) + if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0 + && sg.getStartRes() <= sg.getEndRes())) { // now invert the sequence set, if required - empty selection implies // that no hiding is required. @@ -3050,7 +3091,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.expandColSelection(sg, false); viewport.hideAllSelectedSeqs(); viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3066,7 +3108,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.showAllHiddenColumns(); viewport.showAllHiddenSeqs(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3074,7 +3116,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); - alignPanel.paintAlignment(true); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, true); viewport.sendSelection(); } @@ -3095,7 +3138,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, false); } /** @@ -3108,7 +3152,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, false); } /** @@ -3121,7 +3166,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.updateLayout(); + alignPanel.paintAlignment(true, false); } /** @@ -3134,7 +3180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -3147,7 +3193,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -3160,7 +3206,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } public FeatureSettings featureSettings; @@ -3174,9 +3220,15 @@ 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()) @@ -3186,6 +3238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSeqFeatures_actionPerformed(null); } featureSettings = new FeatureSettings(this); + return featureSettings; } /** @@ -3198,7 +3251,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } /** @@ -3229,14 +3282,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, editPane.setEditable(false); StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); - editPane.setText(MessageManager.formatMessage("label.html_content", - new Object[] { contents.toString() })); + editPane.setText( + MessageManager.formatMessage("label.html_content", new Object[] + { contents.toString() })); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); - Desktop.addInternalFrame(frame, MessageManager.formatMessage( - "label.alignment_properties", new Object[] { getTitle() }), - 500, 400); + Desktop.addInternalFrame(frame, MessageManager + .formatMessage("label.alignment_properties", new Object[] + { getTitle() }), 500, 400); } /** @@ -3256,21 +3310,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JInternalFrame frame = new JInternalFrame(); final OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); - Desktop.addInternalFrame(frame, MessageManager.formatMessage( - "label.overview_params", new Object[] { this.getTitle() }), - true, frame.getWidth(), frame.getHeight(), true, true); + Desktop.addInternalFrame(frame, MessageManager + .formatMessage("label.overview_params", new Object[] + { this.getTitle() }), true, frame.getWidth(), frame.getHeight(), + true, true); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + 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) { - @Override - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - overview.dispose(); - alignPanel.setOverviewPanel(null); - }; - }); + frame.addKeyListener(getKeyListeners()[0]); + } alignPanel.setOverviewPanel(overview); } @@ -3325,7 +3385,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 'User Defined' opens a panel to configure or load a * user-defined colour scheme */ - if (ResidueColourScheme.USER_DEFINED.equals(name)) + if (ResidueColourScheme.USER_DEFINED_MENU.equals(name)) { new UserDefinedColours(alignPanel); return; @@ -3335,7 +3395,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * 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); } @@ -3352,7 +3413,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setGlobalColourScheme(cs); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } /** @@ -3361,8 +3422,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void modifyPID_actionPerformed() { - SliderPanel.setPIDSliderSource(alignPanel, - viewport.getResidueShading(), alignPanel.getViewName()); + SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(), + alignPanel.getViewName()); SliderPanel.showPIDSlider(); } @@ -3433,11 +3494,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); - AlignmentSorter.sortByPID(viewport.getAlignment(), viewport - .getAlignment().getSequenceAt(0)); + AlignmentSorter.sortByPID(viewport.getAlignment(), + viewport.getAlignment().getSequenceAt(0)); addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3451,9 +3512,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByID(viewport.getAlignment()); - addHistoryItem(new OrderCommand("ID Sort", oldOrder, - viewport.getAlignment())); - alignPanel.paintAlignment(true); + addHistoryItem( + new OrderCommand("ID Sort", oldOrder, viewport.getAlignment())); + alignPanel.paintAlignment(true, false); } /** @@ -3469,7 +3530,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignmentSorter.sortByLength(viewport.getAlignment()); addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3486,7 +3547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand("Group Sort", oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } /** @@ -3513,8 +3574,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if ((viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { - JvOptionPane.showInternalMessageDialog(this, MessageManager - .getString("label.you_must_select_least_two_sequences"), + JvOptionPane.showInternalMessageDialog(this, + MessageManager.getString( + "label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"), JvOptionPane.WARNING_MESSAGE); } @@ -3534,8 +3596,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.autoCalculateConsensus = autoCalculate.isSelected(); if (viewport.autoCalculateConsensus) { - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } } @@ -3561,7 +3623,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param options * parameters for the distance or similarity calculation */ - void newTreePanel(String type, String modelName, SimilarityParamsI options) + void newTreePanel(String type, String modelName, + SimilarityParamsI options) { String frameTitle = ""; TreePanel tp; @@ -3577,14 +3640,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (_s.getLength() < sg.getEndRes()) { - JvOptionPane - .showMessageDialog( - Desktop.desktop, - MessageManager - .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), - MessageManager - .getString("label.sequences_selection_not_aligned"), - JvOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, + MessageManager.getString( + "label.selected_region_to_tree_may_only_contain_residues_or_gaps"), + MessageManager.getString( + "label.sequences_selection_not_aligned"), + JvOptionPane.WARNING_MESSAGE); return; } @@ -3604,9 +3665,9 @@ 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; @@ -3625,8 +3686,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { - final JMenuItem item = new JMenuItem(MessageManager.formatMessage( - "action.by_title_param", new Object[] { title })); + final JMenuItem item = new JMenuItem(MessageManager + .formatMessage("action.by_title_param", new Object[] + { title })); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { @@ -3639,10 +3701,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // pointers AlignmentSorter.sortBy(viewport.getAlignment(), order); - addHistoryItem(new OrderCommand(order.getName(), oldOrder, viewport - .getAlignment())); + addHistoryItem(new OrderCommand(order.getName(), oldOrder, + viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } }); } @@ -3671,7 +3733,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment());// ,viewport.getSelectionGroup()); addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder, viewport.getAlignment())); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); } }); } @@ -3696,7 +3758,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - if (viewport.getAlignment().getAlignmentAnnotation().hashCode() != _annotationScoreVectorHash) + if (viewport.getAlignment().getAlignmentAnnotation() + .hashCode() != _annotationScoreVectorHash) { sortByAnnotScore.removeAll(); // almost certainly a quicker way to do this - but we keep it simple @@ -3739,8 +3802,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { sortByTreeMenu.removeAll(); - List comps = PaintRefresher.components.get(viewport - .getSequenceSetId()); + List comps = PaintRefresher.components + .get(viewport.getSequenceSetId()); List treePanels = new ArrayList<>(); for (Component comp : comps) { @@ -3785,7 +3848,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.getAlignment())); } - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, false); return true; } @@ -3879,9 +3942,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.select_newick_like_tree_file")); - chooser.setToolTipText(MessageManager.getString("label.load_tree_file")); + chooser.setDialogTitle( + MessageManager.getString("label.select_newick_like_tree_file")); + chooser.setToolTipText( + MessageManager.getString("label.load_tree_file")); int value = chooser.showOpenDialog(null); @@ -3896,20 +3960,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 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); + 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.showMessageDialog(Desktop.desktop, + fin.getWarningMessage(), + MessageManager + .getString("label.possible_problem_with_tree_file"), JvOptionPane.WARNING_MESSAGE); } } @@ -4139,9 +4200,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception e) { - Cache.log - .debug("Exception during web service menu building process.", - e); + Cache.log.debug( + "Exception during web service menu building process.", + e); } } }); @@ -4226,7 +4287,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void actionPerformed(ActionEvent e) { - showProductsFor(af.viewport.getSequenceSelection(), dna, source); + showProductsFor(af.viewport.getSequenceSelection(), dna, + source); } }); showProducts.add(xtype); @@ -4235,9 +4297,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showProducts.setEnabled(showp); } catch (Exception e) { - Cache.log - .warn("canShowProducts threw an exception - please report to help@jalview.org", - e); + Cache.log.warn( + "canShowProducts threw an exception - please report to help@jalview.org", + e); return false; } return showp; @@ -4254,10 +4316,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param source * the database to show cross-references for */ - protected void showProductsFor(final SequenceI[] sel, - final boolean _odna, final String source) + protected void showProductsFor(final SequenceI[] sel, final boolean _odna, + final String source) { - new Thread(CrossRefAction.showProductsFor(sel, _odna, source, this)) + new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this)) .start(); } @@ -4266,20 +4328,20 @@ 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( "Exception during translation. Please report this !", ex); - final String msg = MessageManager - .getString("label.error_when_translating_sequences_submit_bug_report"); + final String msg = MessageManager.getString( + "label.error_when_translating_sequences_submit_bug_report"); final String errorTitle = MessageManager .getString("label.implementation_error") + MessageManager.getString("label.translation_failed"); @@ -4289,8 +4351,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (al == null || al.getHeight() == 0) { - final String msg = MessageManager - .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); + final String msg = MessageManager.getString( + "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, @@ -4300,9 +4362,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT); af.setFileFormat(this.currentFileFormat); - final String newTitle = MessageManager.formatMessage( - "label.translation_of_params", - new Object[] { this.getTitle() }); + final String newTitle = MessageManager + .formatMessage("label.translation_of_params", new Object[] + { this.getTitle(), codeTable.getId() }); af.setTitle(newTitle); if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true)) { @@ -4384,7 +4446,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - List files = new ArrayList<>(); + final AlignFrame thisaf = this; + final List files = new ArrayList<>(); List protocols = new ArrayList<>(); try @@ -4396,145 +4459,161 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (files != null) { - try + new Thread(new Runnable() { - // check to see if any of these files have names matching sequences in - // the alignment - SequenceIdMatcher idm = new SequenceIdMatcher(viewport - .getAlignment().getSequencesArray()); - /** - * Object[] { String,SequenceI} - */ - ArrayList filesmatched = new ArrayList<>(); - ArrayList filesnotmatched = new ArrayList<>(); - for (int i = 0; i < files.size(); i++) + @Override + public void run() { - String file = files.get(i).toString(); - String pdbfn = ""; - DataSourceType protocol = FormatAdapter.checkProtocol(file); - if (protocol == DataSourceType.FILE) - { - File fl = new File(file); - pdbfn = fl.getName(); - } - else if (protocol == DataSourceType.URL) - { - URL url = new URL(file); - pdbfn = url.getFile(); - } - if (pdbfn.length() > 0) + try { - // attempt to find a match in the alignment - SequenceI[] mtch = idm.findAllIdMatches(pdbfn); - int l = 0, c = pdbfn.indexOf("."); - while (mtch == null && c != -1) + // check to see if any of these files have names matching sequences + // in + // the alignment + SequenceIdMatcher idm = new SequenceIdMatcher( + viewport.getAlignment().getSequencesArray()); + /** + * Object[] { String,SequenceI} + */ + ArrayList filesmatched = new ArrayList<>(); + ArrayList filesnotmatched = new ArrayList<>(); + for (int i = 0; i < files.size(); i++) { - do + String file = files.get(i).toString(); + String pdbfn = ""; + DataSourceType protocol = FormatAdapter.checkProtocol(file); + if (protocol == DataSourceType.FILE) { - l = c; - } while ((c = pdbfn.indexOf(".", l)) > l); - if (l > -1) + File fl = new File(file); + pdbfn = fl.getName(); + } + else if (protocol == DataSourceType.URL) { - pdbfn = pdbfn.substring(0, l); + URL url = new URL(file); + pdbfn = url.getFile(); + } + if (pdbfn.length() > 0) + { + // attempt to find a match in the alignment + SequenceI[] mtch = idm.findAllIdMatches(pdbfn); + int l = 0, c = pdbfn.indexOf("."); + while (mtch == null && c != -1) + { + do + { + l = c; + } while ((c = pdbfn.indexOf(".", l)) > l); + if (l > -1) + { + pdbfn = pdbfn.substring(0, l); + } + mtch = idm.findAllIdMatches(pdbfn); + } + if (mtch != null) + { + FileFormatI type = null; + try + { + type = new IdentifyFile().identify(file, protocol); + } catch (Exception ex) + { + type = null; + } + if (type != null && type.isStructureFile()) + { + filesmatched.add(new Object[] { file, protocol, mtch }); + continue; + } + } + // File wasn't named like one of the sequences or wasn't a PDB + // file. + filesnotmatched.add(file); } - mtch = idm.findAllIdMatches(pdbfn); } - if (mtch != null) + int assocfiles = 0; + if (filesmatched.size() > 0) { - FileFormatI type = null; - try + boolean autoAssociate = Cache + .getDefault("AUTOASSOCIATE_PDBANDSEQS", false); + if (!autoAssociate) { - type = new IdentifyFile().identify(file, protocol); - } catch (Exception ex) + String msg = MessageManager.formatMessage( + "label.automatically_associate_structure_files_with_sequences_same_name", + new Object[] + { Integer.valueOf(filesmatched.size()) + .toString() }); + String ttl = MessageManager.getString( + "label.automatically_associate_structure_files_by_name"); + int choice = JvOptionPane.showConfirmDialog(thisaf, msg, + ttl, JvOptionPane.YES_NO_OPTION); + autoAssociate = choice == JvOptionPane.YES_OPTION; + } + if (autoAssociate) { - type = null; + for (Object[] fm : filesmatched) + { + // try and associate + // TODO: may want to set a standard ID naming formalism for + // 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); + if (pe != null) + { + System.err.println("Associated file : " + + ((String) fm[0]) + " with " + + toassoc.getDisplayId(true)); + assocfiles++; + } + } + // TODO: do we need to update overview ? only if features are + // shown I guess + alignPanel.paintAlignment(true, false); + } } - if (type != null && type.isStructureFile()) + else { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; + /* + * add declined structures as sequences + */ + for (Object[] o : filesmatched) + { + filesnotmatched.add((String) o[0]); + } } } - // File wasn't named like one of the sequences or wasn't a PDB file. - filesnotmatched.add(file); - } - } - int assocfiles = 0; - if (filesmatched.size() > 0) - { - if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JvOptionPane - .showConfirmDialog( - this, - MessageManager - .formatMessage( - "label.automatically_associate_structure_files_with_sequences_same_name", - new Object[] { Integer - .valueOf( - filesmatched - .size()) - .toString() }), - MessageManager - .getString("label.automatically_associate_structure_files_by_name"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) - - { - for (Object[] fm : filesmatched) + if (filesnotmatched.size() > 0) { - // try and associate - // TODO: may want to set a standard ID naming formalism for - // associating PDB files which have no IDs. - for (SequenceI toassoc : (SequenceI[]) fm[2]) + if (assocfiles > 0 && (Cache.getDefault( + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) + || JvOptionPane.showConfirmDialog(thisaf, + "" + MessageManager.formatMessage( + "label.ignore_unmatched_dropped_files_info", + new Object[] + { Integer.valueOf( + filesnotmatched.size()) + .toString() }) + + "", + MessageManager.getString( + "label.ignore_unmatched_dropped_files"), + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) { - PDBEntry pe = new AssociatePdbFileWithSeq() - .associatePdbWithSeq((String) fm[0], - (DataSourceType) fm[1], toassoc, false, - Desktop.instance); - if (pe != null) - { - System.err.println("Associated file : " - + ((String) fm[0]) + " with " - + toassoc.getDisplayId(true)); - assocfiles++; - } + return; + } + for (String fn : filesnotmatched) + { + loadJalviewDataFile(fn, null, null, null); } - alignPanel.paintAlignment(true); + } - } - } - if (filesnotmatched.size() > 0) - { - if (assocfiles > 0 - && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane - .showConfirmDialog( - this, - "" - + MessageManager - .formatMessage( - "label.ignore_unmatched_dropped_files_info", - new Object[] { Integer - .valueOf( - filesnotmatched - .size()) - .toString() }) - + "", - MessageManager - .getString("label.ignore_unmatched_dropped_files"), - JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) - { - return; - } - for (String fn : filesnotmatched) + } catch (Exception ex) { - loadJalviewDataFile(fn, null, null, null); + ex.printStackTrace(); } - } - } catch (Exception ex) - { - ex.printStackTrace(); - } + }).start(); } } @@ -4562,9 +4641,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // if the file isn't identified, or not positively identified as some // other filetype (PFAM is default unidentified alignment file type) then // try to parse as annotation. - boolean isAnnotation = (format == null || FileFormat.Pfam - .equals(format)) ? new AnnotationFile() - .annotateAlignmentView(viewport, file, sourceType) : false; + boolean isAnnotation = (format == null + || FileFormat.Pfam.equals(format)) + ? new AnnotationFile().annotateAlignmentView(viewport, + file, sourceType) + : false; if (!isAnnotation) { @@ -4578,25 +4659,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (tcf.annotateAlignment(viewport.getAlignment(), true)) { buildColourMenu(); - changeColour(new TCoffeeColourScheme(viewport.getAlignment())); + changeColour( + new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; - statusBar - .setText(MessageManager - .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); + statusBar.setText(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, - tcf.getWarningMessage() == null ? MessageManager - .getString("label.check_file_matches_sequence_ids_alignment") - : tcf.getWarningMessage(), - MessageManager - .getString("label.problem_reading_tcoffee_score_file"), - JvOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, + tcf.getWarningMessage() == null + ? MessageManager.getString( + "label.check_file_matches_sequence_ids_alignment") + : tcf.getWarningMessage(), + MessageManager.getString( + "label.problem_reading_tcoffee_score_file"), + JvOptionPane.WARNING_MESSAGE); } } else @@ -4605,9 +4685,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception x) { - Cache.log - .debug("Exception when processing data source as T-COFFEE score file", - x); + Cache.log.debug( + "Exception when processing data source as T-COFFEE score file", + x); tcf = null; } if (tcf == null) @@ -4621,14 +4701,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (FileFormat.ScoreMatrix == format) { - ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file, - sourceType)); + ScoreMatrixFile sm = new ScoreMatrixFile( + new FileParse(file, sourceType)); sm.parse(); // todo: i18n this message - statusBar - .setText(MessageManager.formatMessage( - "label.successfully_loaded_matrix", - sm.getMatrixName())); + statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_matrix", + sm.getMatrixName())); } else if (FileFormat.Jnet.equals(format)) { @@ -4636,11 +4715,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); - SequenceI repseq = viewport.getAlignment().getSequenceAt(0); - viewport.getAlignment().setSeqrep(repseq); - HiddenColumns cs = new HiddenColumns(); - cs.hideInsertionsFor(repseq); - viewport.getAlignment().setHiddenColumns(cs); + viewport.getAlignment().setupJPredAlignment(); isAnnotation = true; } // else if (IdentifyFile.FeaturesFile.equals(format)) @@ -4648,7 +4723,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (parseFeaturesFile(file, sourceType)) { - alignPanel.paintAlignment(true); + SplitFrame splitFrame = (SplitFrame) getSplitViewContainer(); + if (splitFrame != null) + { + splitFrame.repaint(); + } + else + { + alignPanel.paintAlignment(true, true); + } } } else @@ -4663,7 +4746,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.adjustAnnotationHeight(); viewport.updateSequenceIdColours(); buildSortByAnnotationScoresMenu(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } catch (Exception ex) { @@ -4678,11 +4761,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } new OOMWarning( "loading data " - + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard." - : "using " + sourceType + " from " + file) + + (sourceType != null + ? (sourceType == DataSourceType.PASTE + ? "from clipboard." + : "using " + sourceType + " from " + + file) : ".") - + (format != null ? "(parsing as '" + format - + "' file)" : ""), oom, Desktop.desktop); + + (format != null + ? "(parsing as '" + format + "' file)" + : ""), + oom, Desktop.desktop); } } @@ -4699,6 +4787,21 @@ 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(); + } + } + } /* @@ -4733,7 +4836,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final AlignViewportI peer = viewport.getCodingComplement(); if (peer != null) { - AlignFrame linkedAlignFrame = ((AlignViewport) peer).getAlignPanel().alignFrame; + AlignFrame linkedAlignFrame = ((AlignViewport) peer) + .getAlignPanel().alignFrame; if (linkedAlignFrame.tabbedPane.getTabCount() > index) { linkedAlignFrame.tabbedPane.setSelectedIndex(index); @@ -4755,7 +4859,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (reply != null) { - viewport.viewName = reply; + viewport.setViewName(reply); // TODO warn if reply is in getExistingViewNames()? tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply); } @@ -4848,30 +4952,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // here final JMenu rfetch = new JMenu( MessageManager.getString("action.fetch_db_references")); - rfetch.setToolTipText(MessageManager - .getString("label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences")); + rfetch.setToolTipText(MessageManager.getString( + "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences")); webService.add(rfetch); final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem( MessageManager.getString("option.trim_retrieved_seqs")); - trimrs.setToolTipText(MessageManager - .getString("label.trim_retrieved_sequences")); - trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true)); + trimrs.setToolTipText( + MessageManager.getString("label.trim_retrieved_sequences")); + trimrs.setSelected( + Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true)); trimrs.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { trimrs.setSelected(trimrs.isSelected()); - Cache.setProperty("TRIM_FETCHED_DATASET_SEQS", + Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, Boolean.valueOf(trimrs.isSelected()).toString()); }; }); rfetch.add(trimrs); JMenuItem fetchr = new JMenuItem( MessageManager.getString("label.standard_databases")); - fetchr.setToolTipText(MessageManager - .getString("label.fetch_embl_uniprot")); + fetchr.setToolTipText( + MessageManager.getString("label.fetch_embl_uniprot")); fetchr.addActionListener(new ActionListener() { @@ -4885,14 +4990,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { boolean isNucleotide = alignPanel.alignFrame.getViewport() .getAlignment().isNucleotide(); - DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av - .getSequenceSelection(), alignPanel.alignFrame, null, + DBRefFetcher dbRefFetcher = new DBRefFetcher( + alignPanel.av.getSequenceSelection(), + alignPanel.alignFrame, null, alignPanel.alignFrame.featureSettings, isNucleotide); dbRefFetcher.addListener(new FetchFinishedListenerI() { @Override public void finished() { + + for (FeatureSettingsModelI srcSettings : dbRefFetcher + .getFeatureSettingsModels()) + { + + alignPanel.av.mergeFeaturesStyle(srcSettings); + } AlignFrame.this.setMenusForViewport(); } }); @@ -4978,6 +5091,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void finished() { + FeatureSettingsModelI srcSettings = dassource[0] + .getFeatureColourScheme(); + alignPanel.av.mergeFeaturesStyle( + srcSettings); AlignFrame.this.setMenusForViewport(); } }); @@ -4989,8 +5106,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( - "label.fetch_retrieve_from", - new Object[] { src.getDbName() }))); + "label.fetch_retrieve_from", new Object[] + { src.getDbName() }))); dfetch.add(fetchr); comp++; } @@ -5000,9 +5117,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .toArray(new DbSourceProxy[0]); // fetch all entry DbSourceProxy src = otherdb.get(0); - fetchr = new JMenuItem(MessageManager.formatMessage( - "label.fetch_all_param", - new Object[] { src.getDbSource() })); + fetchr = new JMenuItem(MessageManager + .formatMessage("label.fetch_all_param", new Object[] + { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { @Override @@ -5040,30 +5157,33 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage( "label.fetch_retrieve_from_all_sources", - new Object[] { - Integer.valueOf(otherdb.size()) - .toString(), src.getDbSource(), - src.getDbName() }))); + new Object[] + { Integer.valueOf(otherdb.size()) + .toString(), + src.getDbSource(), src.getDbName() }))); dfetch.add(fetchr); comp++; // and then build the rest of the individual menus ifetch = new JMenu(MessageManager.formatMessage( - "label.source_from_db_source", - new Object[] { src.getDbSource() })); + "label.source_from_db_source", new Object[] + { src.getDbSource() })); icomp = 0; String imname = null; int i = 0; for (DbSourceProxy sproxy : otherdb) { String dbname = sproxy.getDbName(); - String sname = dbname.length() > 5 ? dbname.substring(0, - 5) + "..." : dbname; - String msname = dbname.length() > 10 ? dbname.substring( - 0, 10) + "..." : dbname; + String sname = dbname.length() > 5 + ? dbname.substring(0, 5) + "..." + : dbname; + String msname = dbname.length() > 10 + ? dbname.substring(0, 10) + "..." + : dbname; if (imname == null) { - imname = MessageManager.formatMessage( - "label.from_msname", new Object[] { sname }); + imname = MessageManager + .formatMessage("label.from_msname", new Object[] + { sname }); } fetchr = new JMenuItem(msname); final DbSourceProxy[] dassrc = { sproxy }; @@ -5102,8 +5222,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - fetchr.setToolTipText("" - + MessageManager.formatMessage( + fetchr.setToolTipText( + "" + MessageManager.formatMessage( "label.fetch_retrieve_from", new Object[] { dbname })); ifetch.add(fetchr); @@ -5178,7 +5298,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { viewport.setShowUnconserved(showNonconservedMenuItem.getState()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /* @@ -5267,7 +5387,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, + viewport.needToUpdateStructureViews()); } } @@ -5279,7 +5400,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getAlignment().setSeqrep(null); PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(true, true); } } @@ -5288,6 +5409,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (avc.createGroup()) { + if (applyAutoAnnotationSettings.isSelected()) + { + alignPanel.updateAnnotation(true, false); + } alignPanel.alignmentChanged(); } } @@ -5308,17 +5433,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void setDisplayedView(AlignmentPanel alignmentPanel) { - if (!viewport.getSequenceSetId().equals( - alignmentPanel.av.getSequenceSetId())) + if (!viewport.getSequenceSetId() + .equals(alignmentPanel.av.getSequenceSetId())) { - throw new Error( - MessageManager - .getString("error.implementation_error_cannot_show_view_alignment_frame")); + throw new Error(MessageManager.getString( + "error.implementation_error_cannot_show_view_alignment_frame")); } - if (tabbedPane != null - && tabbedPane.getTabCount() > 0 - && alignPanels.indexOf(alignmentPanel) != tabbedPane - .getSelectedIndex()) + if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels + .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex()) { tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); } @@ -5372,7 +5494,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder()); this.alignPanel.av .setShowAutocalculatedAbove(isShowAutoCalculatedAbove()); - alignPanel.paintAlignment(true); + alignPanel.paintAlignment(false, false); } /** @@ -5381,7 +5503,9 @@ 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; } /** @@ -5421,15 +5545,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // show a warning dialog no mapped cDNA return; } - AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs - .size()])); + AlignmentI cdna = new Alignment( + cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()])); GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); cdna.alignAs(alignment); String newtitle = "cDNA " + MessageManager.getString("label.for") + " " + this.title; - Desktop.addInternalFrame(alignFrame, newtitle, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); } /** @@ -5462,8 +5586,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, al = dna.reverseCdna(complement); viewport.addAlignment(al, ""); addHistoryItem(new EditCommand( - MessageManager.getString("label.add_sequences"), - Action.PASTE, al.getSequencesArray(), 0, al.getWidth(), + MessageManager.getString("label.add_sequences"), Action.PASTE, + al.getSequencesArray(), 0, al.getWidth(), viewport.getAlignment())); } catch (Exception ex) { @@ -5490,12 +5614,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { System.err.println((ex.toString())); - JvOptionPane - .showInternalMessageDialog(Desktop.desktop, MessageManager - .getString("label.couldnt_run_groovy_script"), - MessageManager - .getString("label.groovy_support_failed"), - JvOptionPane.ERROR_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.getString("label.couldnt_run_groovy_script"), + MessageManager.getString("label.groovy_support_failed"), + JvOptionPane.ERROR_MESSAGE); } } else @@ -5535,9 +5657,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // include key modifier check in case user selects from menu avc.markHighlightedColumns( - (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, - true, - (actionEvent.getModifiers() & (ActionEvent.META_MASK | ActionEvent.CTRL_MASK)) != 0); + (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true, + (actionEvent.getModifiers() & (ActionEvent.META_MASK + | ActionEvent.CTRL_MASK)) != 0); } /** @@ -5552,15 +5674,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, colourMenu.add(textColour); colourMenu.addSeparator(); - ColourMenuHelper.addMenuItems(colourMenu, this, + 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); @@ -5577,6 +5700,41 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new CalculationChooser(AlignFrame.this); } } + + @Override + protected void loadVcf_actionPerformed() + { + JalviewFileChooser chooser = new JalviewFileChooser( + Cache.getProperty("LAST_DIRECTORY")); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file")); + chooser.setToolTipText(MessageManager.getString("label.load_vcf_file")); + + int value = chooser.showOpenDialog(null); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + Cache.setProperty("LAST_DIRECTORY", choice); + SequenceI[] seqs = viewport.getAlignment().getSequencesArray(); + new VCFLoader(choice).loadVCF(seqs, this); + } + + } + + private Rectangle lastFeatureSettingsBounds = null; + + @Override + public void setFeatureSettingsGeometry(Rectangle bounds) + { + lastFeatureSettingsBounds = bounds; + } + + @Override + public Rectangle getFeatureSettingsGeometry() + { + return lastFeatureSettingsBounds; + } } class PrintThread extends Thread