X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=0f47cca4eb6a429eb4c9e6bbf043662e68dbc724;hb=2e7da637a195ff484f92a333675284f071657cd6;hp=92316b3e1dc3474b63715a80ffbe8b7836da028a;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 92316b3..0f47cca 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -153,9 +153,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public AlignmentPanel alignPanel; AlignViewport viewport; - + public AlignViewControllerI avc; - Vector alignPanels = new Vector(); @@ -264,15 +263,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int width, int height, String sequenceSetId, String viewId) { setSize(width, height); - viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); - - alignPanel = new AlignmentPanel(this, viewport); if (al.getDataset() == null) { al.setDataset(null); } + viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); + + alignPanel = new AlignmentPanel(this, viewport); + + addAlignmentPanel(alignPanel, true); init(); } @@ -299,7 +300,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ void init() { - avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); + avc = new jalview.controller.AlignViewController(this, viewport, + alignPanel); if (viewport.getAlignmentConservationAnnotation() == null) { BLOSUM62Colour.setEnabled(false); @@ -332,6 +334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setMenusFromViewport(viewport); buildSortByAnnotationScoresMenu(); buildTreeMenu(); + if (viewport.wrapAlignment) { wrapMenuItem_actionPerformed(null); @@ -343,7 +346,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } addKeyListener(); - + } /** @@ -489,7 +492,9 @@ 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.seqPanel.seqCanvas.cursorX = viewport.startRes; @@ -501,14 +506,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_F1: try { - ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); - java.net.URL url = javax.help.HelpSet.findHelpSet(cl, - "help/help"); - javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); - - javax.help.HelpBroker hb = hs.createHelpBroker(); - hb.setCurrentID("home"); - hb.setDisplayed(true); + Help.showHelpWindow(); } catch (Exception ex) { ex.printStackTrace(); @@ -570,7 +568,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel) { ap.alignFrame = this; - avc = new jalview.controller.AlignViewController(this, viewport, alignPanel); + avc = new jalview.controller.AlignViewController(this, viewport, + alignPanel); alignPanels.addElement(ap); @@ -724,6 +723,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, scaleLeft.setVisible(av.wrapAlignment); scaleRight.setVisible(av.wrapAlignment); annotationPanelMenuItem.setState(av.showAnnotation); + /* + * Show/hide all annotations only enabled if annotation panel is shown + */ + showAllAnnotations.setEnabled(annotationPanelMenuItem.getState()); + hideAllAnnotations.setEnabled(annotationPanelMenuItem.getState()); viewBoxesMenuItem.setSelected(av.showBoxes); viewTextMenuItem.setSelected(av.showText); showNonconservedMenuItem.setSelected(av.getShowUnconserved()); @@ -814,14 +818,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { - throw new Error( - "call setProgressBar before registering the progress bar's handler."); + throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler")); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); if (handler.canCancel()) { - JButton cancel = new JButton(MessageManager.getString("action.cancel")); + JButton cancel = new JButton( + MessageManager.getString("action.cancel")); final IProgressIndicator us = this; cancel.addActionListener(new ActionListener() { @@ -830,10 +834,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar( - "Cancelled " - + ((JLabel) progressPanel.getComponent(0)) - .getText(), id); + us.setProgressBar(MessageManager.formatMessage("label.cancelled_params", new String[]{((JLabel) progressPanel.getComponent(0)).getText()}), id); } }); progressPanel.add(cancel, BorderLayout.EAST); @@ -855,9 +856,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void setStatus(String text) { + public void setStatus(String text) + { statusBar.setText(text); }; + /* * Added so Castor Mapping file can obtain Jalview Version */ @@ -994,7 +997,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat, false); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save Alignment to file"); + chooser.setDialogTitle(MessageManager.getString("label.save_alignment_to_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -1004,9 +1007,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat = chooser.getSelectedFormat(); if (currentFileFormat == null) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.select_file_format_before_saving"), - MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE); + JOptionPane + .showInternalMessageDialog( + Desktop.desktop, + MessageManager + .getString("label.select_file_format_before_saving"), + MessageManager + .getString("label.file_format_not_specified"), + JOptionPane.WARNING_MESSAGE); value = chooser.showSaveDialog(this); return; } @@ -1042,8 +1050,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, success = new Jalview2XML().SaveAlignment(this, file, shortName); - statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format})); - + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", new String[] + { fileName, format })); } else @@ -1064,8 +1073,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int reply = JOptionPane .showInternalConfirmDialog( Desktop.desktop, - MessageManager.getString("label.alignment_contains_hidden_columns"), - MessageManager.getString("action.save_omit_hidden_columns"), + MessageManager + .getString("label.alignment_contains_hidden_columns"), + MessageManager + .getString("action.save_omit_hidden_columns"), JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); @@ -1095,7 +1106,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, out.print(output); out.close(); this.setTitle(file); - statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format})); + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", + new String[] + { fileName, format })); } catch (Exception ex) { success = false; @@ -1106,8 +1120,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { - JOptionPane.showInternalMessageDialog(this, MessageManager.formatMessage("label.couldnt_save_file", new String[]{fileName}), - MessageManager.getString("label.error_saving_file"), JOptionPane.WARNING_MESSAGE); + JOptionPane.showInternalMessageDialog(this, MessageManager + .formatMessage("label.couldnt_save_file", new String[] + { fileName }), MessageManager + .getString("label.error_saving_file"), + JOptionPane.WARNING_MESSAGE); } return success; @@ -1144,8 +1161,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int reply = JOptionPane .showInternalConfirmDialog( Desktop.desktop, - MessageManager.getString("label.alignment_contains_hidden_columns"), - MessageManager.getString("action.save_omit_hidden_columns"), + MessageManager + .getString("label.alignment_contains_hidden_columns"), + MessageManager + .getString("action.save_omit_hidden_columns"), JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE); @@ -1163,8 +1182,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), viewport.getAlignment(), omitHidden, viewport.getColumnSelection())); - Desktop.addInternalFrame(cap, - MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500); + Desktop.addInternalFrame(cap, MessageManager.formatMessage( + "label.alignment_output_command", new String[] + { e.getActionCommand() }), 600, 500); } catch (OutOfMemoryError oom) { new OOMWarning("Outputting alignment as " + e.getActionCommand(), oom); @@ -1260,8 +1280,10 @@ 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); @@ -1361,7 +1383,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { undoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.historyList.peek(); - undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()})); + undoMenuItem.setText(MessageManager.formatMessage( + "label.undo_command", new String[] + { command.getDescription() })); } else { @@ -1374,7 +1398,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, redoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.redoList.peek(); - redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()})); + redoMenuItem.setText(MessageManager.formatMessage( + "label.redo_command", new String[] + { command.getDescription() })); } else { @@ -1707,7 +1733,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; - statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()})); + statusBar.setText(MessageManager.formatMessage( + "label.copied_sequences_to_clipboard", new String[] + { Integer.valueOf(seqs.length).toString() })); } /** @@ -1914,7 +1942,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // ///// // ADD HISTORY ITEM // - addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE, + addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment)); } // Add any annotations attached to sequences @@ -2065,59 +2093,61 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override protected void expand_newalign(ActionEvent e) { - try { - AlignmentI alignment = AlignmentUtils.expandContext(getViewport().getAlignment(), -1); - AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - String newtitle = new String("Flanking alignment"); - - if (Desktop.jalviewClipboard != null - && Desktop.jalviewClipboard[2] != null) + try { - Vector hc = (Vector) Desktop.jalviewClipboard[2]; - for (int i = 0; i < hc.size(); i++) + AlignmentI alignment = AlignmentUtils.expandContext(getViewport() + .getAlignment(), -1); + AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + String newtitle = new String("Flanking alignment"); + + if (Desktop.jalviewClipboard != null + && Desktop.jalviewClipboard[2] != null) { - int[] region = (int[]) hc.elementAt(i); - af.viewport.hideColumns(region[0], region[1]); + Vector hc = (Vector) Desktop.jalviewClipboard[2]; + for (int i = 0; i < hc.size(); i++) + { + int[] region = (int[]) hc.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } } - } - // >>>This is a fix for the moment, until a better solution is - // found!!<<< - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() - .transferSettings( - alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); + // >>>This is a fix for the moment, until a better solution is + // found!!<<< + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + .transferSettings( + alignPanel.seqPanel.seqCanvas.getFeatureRenderer()); - // TODO: maintain provenance of an alignment, rather than just make the - // title a concatenation of operations. - { - if (title.startsWith("Copied sequences")) - { - newtitle = title; - } - else + // TODO: maintain provenance of an alignment, rather than just make the + // title a concatenation of operations. { - newtitle = newtitle.concat("- from " + title); + if (title.startsWith("Copied sequences")) + { + newtitle = title; + } + else + { + newtitle = newtitle.concat("- from " + title); + } } - } - Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, - DEFAULT_HEIGHT); + Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } catch (Exception ex) { ex.printStackTrace(); System.out.println("Exception whilst pasting: " + ex); // could be anything being pasted in here - } - catch (OutOfMemoryError oom) + } catch (OutOfMemoryError oom) { new OOMWarning("Viewing flanking region of alignment", oom); } } + /** * DOCUMENT ME! * @@ -2147,17 +2177,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - Vector seqs = new Vector(); + List seqs = new ArrayList(sg.getSize()); SequenceI seq; for (int i = 0; i < sg.getSize(); i++) { seq = sg.getSequenceAt(i); - seqs.addElement(seq); + seqs.add(seq); } - // If the cut affects all sequences, remove highlighted columns + // If the cut affects all sequences, warn, remove highlighted columns if (sg.getSize() == viewport.getAlignment().getHeight()) { + int confirm = JOptionPane.showConfirmDialog(this, + MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ + MessageManager.getString("label.delete_all"), // $NON-NLS-1$ + JOptionPane.OK_CANCEL_OPTION); + + if (confirm == JOptionPane.CANCEL_OPTION + || confirm == JOptionPane.CLOSED_OPTION) + { + return; + } viewport.getColumnSelection().removeElements(sg.getStartRes(), sg.getEndRes() + 1); } @@ -2165,13 +2205,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SequenceI[] cut = new SequenceI[seqs.size()]; for (int i = 0; i < seqs.size(); i++) { - cut[i] = (SequenceI) seqs.elementAt(i); + cut[i] = seqs.get(i); } /* * //ADD HISTORY ITEM */ - addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut, + addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1, viewport.getAlignment())); @@ -2201,7 +2241,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void deleteGroups_actionPerformed(ActionEvent e) { - if (avc.deleteGroups()) { + if (avc.deleteGroups()) + { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); @@ -2359,7 +2400,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getSelectionGroup()); } - 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); @@ -2407,7 +2450,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); - statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()})); + statusBar.setText(MessageManager.formatMessage( + "label.removed_empty_columns", new String[] + { Integer.valueOf(removeGapCols.getSize()).toString() })); // This is to maintain viewport position on first residue // of first sequence @@ -2570,7 +2615,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, boolean addFirstIndex = false; if (viewTitle == null || viewTitle.trim().length() == 0) { - viewTitle = "View"; + viewTitle = MessageManager.getString("action.view"); addFirstIndex = true; } else @@ -2602,7 +2647,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addAlignmentPanel(newap, true); newap.alignmentChanged(); - + if (alignPanels.size() == 2) { viewport.gatherViewsHere = true; @@ -2997,16 +3042,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * DOCUMENT ME! + * Action on toggle of the 'Show annotations' menu item. This shows or hides + * the annotations panel as a whole. + * + * The options to show/hide all annotations should be enabled when the panel + * is shown, and disabled when the panel is hidden. * * @param e - * DOCUMENT ME! */ @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); + final boolean setVisible = annotationPanelMenuItem.isSelected(); + viewport.setShowAnnotation(setVisible); + alignPanel.setAnnotationVisible(setVisible); + this.showAllAnnotations.setEnabled(setVisible); + this.hideAllAnnotations.setEnabled(setVisible); } @Override @@ -3016,11 +3067,15 @@ 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 String[]{contents.toString()})); + editPane.setText(MessageManager.formatMessage("label.html_content", + new String[] + { contents.toString() })); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); - Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}), 500, 400); + Desktop.instance.addInternalFrame(frame, MessageManager.formatMessage( + "label.alignment_properties", new String[] + { getTitle() }), 500, 400); } /** @@ -3040,8 +3095,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JInternalFrame frame = new JInternalFrame(); OverviewPanel overview = new OverviewPanel(alignPanel); frame.setContentPane(overview); - Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}), - frame.getWidth(), frame.getHeight()); + Desktop.addInternalFrame(frame, MessageManager.formatMessage( + "label.overview_params", new String[] + { this.getTitle() }), frame.getWidth(), frame.getHeight()); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() @@ -3423,7 +3479,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void userDefinedColour_actionPerformed(ActionEvent e) { - if (e.getActionCommand().equals(MessageManager.getString("action.user_defined"))) + if (e.getActionCommand().equals( + MessageManager.getString("action.user_defined"))) { new UserDefinedColours(alignPanel, null); } @@ -3472,8 +3529,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, - MessageManager.getString("label.remove_from_default_list"), - MessageManager.getString("label.remove_user_defined_colour"), + MessageManager + .getString("label.remove_from_default_list"), + MessageManager + .getString("label.remove_user_defined_colour"), JOptionPane.YES_NO_OPTION); if (option == JOptionPane.YES_OPTION) { @@ -3624,15 +3683,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if ((viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { - JOptionPane.showInternalMessageDialog(this, - MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"), + JOptionPane.showInternalMessageDialog(this, MessageManager + .getString("label.you_must_select_least_two_sequences"), + MessageManager.getString("label.invalid_selection"), JOptionPane.WARNING_MESSAGE); } else { JInternalFrame frame = new JInternalFrame(); frame.setContentPane(new PairwiseAlignPanel(viewport)); - Desktop.addInternalFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500); + Desktop.addInternalFrame(frame, + MessageManager.getString("action.pairwise_alignment"), 600, + 500); } } @@ -3650,10 +3712,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getSelectionGroup().getSize() > 0)) || (viewport.getAlignment().getHeight() < 4)) { - JOptionPane.showInternalMessageDialog(this, - MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"), - MessageManager.getString("label.sequence_selection_insufficient"), - JOptionPane.WARNING_MESSAGE); + JOptionPane + .showInternalMessageDialog( + this, + MessageManager + .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), + MessageManager + .getString("label.sequence_selection_insufficient"), + JOptionPane.WARNING_MESSAGE); return; } @@ -3754,8 +3820,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - MessageManager.getString("label.you_need_more_two_sequences_selected_build_tree"), - MessageManager.getString("label.not_enough_sequences"), JOptionPane.WARNING_MESSAGE); + MessageManager + .getString("label.you_need_more_two_sequences_selected_build_tree"), + MessageManager + .getString("label.not_enough_sequences"), + JOptionPane.WARNING_MESSAGE); return; } @@ -3769,8 +3838,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - MessageManager.getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), - MessageManager.getString("label.sequences_selection_not_aligned"), + MessageManager + .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), + MessageManager + .getString("label.sequences_selection_not_aligned"), JOptionPane.WARNING_MESSAGE); return; @@ -3788,8 +3859,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"), - MessageManager.getString("label.sequences_not_aligned"), + MessageManager + .getString("label.sequences_must_be_aligned_before_creating_tree"), + MessageManager + .getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE); return; @@ -3826,7 +3899,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void addSortByOrderMenuItem(String title, final AlignmentOrder order) { - final JMenuItem item = new JMenuItem("by " + title); + final JMenuItem item = new JMenuItem(MessageManager.formatMessage("action.by_title_param", new String[]{title})); sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { @@ -3944,15 +4017,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { calculateTree.removeAll(); // build the calculate menu - - for (final String type:new String[] {"NJ", "AV"}) + + for (final String type : new String[] + { "NJ", "AV" }) { - String treecalcnm = MessageManager.getString("label.tree_calc_"+type.toLowerCase()); - for (final Object pwtype: ResidueProperties.scoreMatrices.keySet()) + String treecalcnm = MessageManager.getString("label.tree_calc_" + + type.toLowerCase()); + for (final Object pwtype : ResidueProperties.scoreMatrices.keySet()) { JMenuItem tm = new JMenuItem(); ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype); - if (sm.isProtein()==!viewport.getAlignment().isNucleotide()) + if (sm.isProtein() == !viewport.getAlignment().isNucleotide()) { String smn = MessageManager.getStringOrReturn( "label.score_model_", sm.getName()); @@ -3961,6 +4036,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tm.setText(title);// tm.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { NewTreePanel(type, (String) pwtype, title); @@ -4115,7 +4191,8 @@ 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.setDialogTitle(MessageManager + .getString("label.select_newick_like_tree_file")); chooser.setToolTipText(MessageManager.getString("label.load_tree_file")); int value = chooser.showOpenDialog(null); @@ -4131,14 +4208,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { - JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), - MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE); + JOptionPane + .showMessageDialog( + Desktop.desktop, + ex.getMessage(), + MessageManager + .getString("label.problem_reading_tree_file"), + JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin != null && fin.hasWarningMessage()) { - JOptionPane.showMessageDialog(Desktop.desktop, - fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"), + JOptionPane.showMessageDialog(Desktop.desktop, fin + .getWarningMessage(), MessageManager + .getString("label.possible_problem_with_tree_file"), JOptionPane.WARNING_MESSAGE); } } @@ -4243,7 +4326,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void run() { - final List legacyItems=new ArrayList(); + final List legacyItems = new ArrayList(); try { System.err.println("Building ws menu again " @@ -4266,6 +4349,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); final JMenu analymenu = new JMenu("Analysis"); final JMenu dismenu = new JMenu("Protein Disorder"); + // final JMenu msawsmenu = new + // JMenu(MessageManager.getString("label.alignment")); + // final JMenu secstrmenu = new + // JMenu(MessageManager.getString("label.secondary_structure_prediction")); + // final JMenu seqsrchmenu = new + // JMenu(MessageManager.getString("label.sequence_database_search")); + // final JMenu analymenu = new + // JMenu(MessageManager.getString("label.analysis")); + // final JMenu dismenu = new + // JMenu(MessageManager.getString("label.protein_disorder")); // JAL-940 - only show secondary structure prediction services from // the legacy server if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) @@ -4276,7 +4369,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // be // stored or retrieved from elsewhere // No MSAWS used any more: - // Vector msaws = null; // (Vector) Discoverer.services.get("MsaWS"); + // Vector msaws = null; // (Vector) + // Discoverer.services.get("MsaWS"); Vector secstrpr = (Vector) Discoverer.services .get("SecStrPred"); if (secstrpr != null) @@ -4288,17 +4382,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .get(i); jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer .getServiceClient(sh); - int p=secstrmenu.getItemCount(); + int p = secstrmenu.getItemCount(); impl.attachWSMenuEntry(secstrmenu, me); - int q=secstrmenu.getItemCount(); - for (int litm=p;litm" - + JvSwingUtils.wrapTooltip("Retrieve from " - + src.getDbName()) + ""); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{src.getDbName()}))); dfetch.add(fetchr); comp++; } @@ -5315,7 +5449,9 @@ 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 String[]{src.getDbSource()})); + fetchr = new JMenuItem(MessageManager.formatMessage( + "label.fetch_all_param", new String[] + { src.getDbSource() })); fetchr.addActionListener(new ActionListener() { @Override @@ -5336,15 +5472,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } }); - fetchr.setToolTipText("" - + JvSwingUtils.wrapTooltip("Retrieve from all " - + otherdb.size() + " sources in " - + src.getDbSource() + "
First is :" - + src.getDbName()) + ""); + fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.fetch_retrieve_from_all_sources", new String[]{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("Sources from " + src.getDbSource()); + ifetch = new JMenu(MessageManager.formatMessage("label.source_from_db_source", new String[]{src.getDbSource()})); icomp = 0; String imname = null; int i = 0; @@ -5357,7 +5489,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, 0, 10) + "..." : dbname; if (imname == null) { - imname = "from '" + sname + "'"; + imname = MessageManager.formatMessage("label.from_msname", new String[]{sname}); } fetchr = new JMenuItem(msname); final DbSourceProxy[] dassrc = @@ -5384,13 +5516,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); fetchr.setToolTipText("" - + JvSwingUtils.wrapTooltip("Retrieve from " - + dbname) + ""); + + MessageManager.formatMessage("label.fetch_retrieve_from", new String[]{dbname})); ifetch.add(fetchr); ++i; if (++icomp >= mcomp || i == (otherdb.size())) { - ifetch.setText(MessageManager.formatMessage("label.source_to_target",imname,sname)); + ifetch.setText(MessageManager.formatMessage( + "label.source_to_target", imname, sname)); dfetch.add(ifetch); ifetch = new JMenu(); imname = null; @@ -5402,7 +5534,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ++dbi; if (comp >= mcomp || dbi >= (dbclasses.length)) { - dfetch.setText(MessageManager.formatMessage("label.source_to_target",mname,dbclass)); + dfetch.setText(MessageManager.formatMessage( + "label.source_to_target", mname, dbclass)); rfetch.add(dfetch); dfetch = new JMenu(); mname = null; @@ -5540,7 +5673,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { - if (avc.makeGroupsFromSelection()) { + if (avc.makeGroupsFromSelection()) + { PaintRefresher.Refresh(this, viewport.getSequenceSetId()); alignPanel.updateAnnotation(); alignPanel.paintAlignment(true); @@ -5575,8 +5709,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!viewport.getSequenceSetId().equals( alignmentPanel.av.getSequenceSetId())) { - throw new Error( - "Implementation error: cannot show a view from another alignment in an AlignFrame."); + throw new Error(MessageManager.getString("error.implementation_error_cannot_show_view_alignment_frame")); } if (tabbedPane != null & alignPanels.indexOf(alignmentPanel) != tabbedPane @@ -5585,6 +5718,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel)); } } + + /** + * Action on selection of menu option to Show or Hide all annotations. + * + * @param visibile + */ + @Override + protected void setAllAnnotationsVisibility(boolean visible) + { + for (AlignmentAnnotation aa : alignPanel.getAlignment() + .getAlignmentAnnotation()) + { + aa.visible = visible; + } + this.alignPanel.paintAlignment(true); + } } class PrintThread extends Thread