X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=62fd29dd674a958a61f5b43b3efc7101933a00c4;hb=dd3059c62cd80e712c0f6df866d6d69588e5f3eb;hp=382ccda0352e535dcac82bcadadb36dcd7881c1f;hpb=8a3c31b03ed98321d1d450b658d26d50a7aa0ae6;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java old mode 100755 new mode 100644 index 382ccda..62fd29d --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -76,6 +76,7 @@ import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; +import jalview.util.MessageManager; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -481,8 +482,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, case KeyEvent.VK_F2: viewport.cursorMode = !viewport.cursorMode; - statusBar.setText("Keyboard editing mode is " - + (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; @@ -814,7 +814,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); if (handler.canCancel()) { - JButton cancel = new JButton("Cancel"); + JButton cancel = new JButton(MessageManager.getString("action.cancel")); final IProgressIndicator us = this; cancel.addActionListener(new ActionListener() { @@ -994,8 +994,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (currentFileFormat == null) { JOptionPane.showInternalMessageDialog(Desktop.desktop, - "You must select a file format before saving!", - "File format not specified", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.select_file_format_before_saving"), + MessageManager.getString("label.file_format_not_specified"), JOptionPane.WARNING_MESSAGE); value = chooser.showSaveDialog(this); return; } @@ -1031,8 +1031,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, success = new Jalview2XML().SaveAlignment(this, file, shortName); - statusBar.setText("Successfully saved to file: " + fileName + " in " - + format + " format."); + statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format})); + } else @@ -1053,9 +1053,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int reply = JOptionPane .showInternalConfirmDialog( Desktop.desktop, - "The Alignment contains hidden columns." - + "\nDo you want to save only the visible alignment?", - "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); @@ -1085,8 +1084,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, out.print(output); out.close(); this.setTitle(file); - statusBar.setText("Successfully saved to file: " + fileName - + " in " + format + " format."); + statusBar.setText(MessageManager.formatMessage("label.successfully_saved_to_file_in_format",new String[]{fileName, format})); } catch (Exception ex) { success = false; @@ -1097,8 +1095,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { - JOptionPane.showInternalMessageDialog(this, "Couldn't save file: " - + fileName, "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; @@ -1135,9 +1133,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int reply = JOptionPane .showInternalConfirmDialog( Desktop.desktop, - "The Alignment contains hidden columns." - + "\nDo you want to output only the visible alignment?", - "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); @@ -1353,12 +1350,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { undoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.historyList.peek(); - undoMenuItem.setText("Undo " + command.getDescription()); + undoMenuItem.setText(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()})); } else { undoMenuItem.setEnabled(false); - undoMenuItem.setText("Undo"); + undoMenuItem.setText(MessageManager.getString("action.undo")); } if (viewport.redoList.size() > 0) @@ -1366,12 +1363,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, redoMenuItem.setEnabled(true); CommandI command = (CommandI) viewport.redoList.peek(); - redoMenuItem.setText("Redo " + command.getDescription()); + redoMenuItem.setText(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()})); } else { redoMenuItem.setEnabled(false); - redoMenuItem.setText("Redo"); + redoMenuItem.setText(MessageManager.getString("action.redo")); } } @@ -1699,7 +1696,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.jalviewClipboard = new Object[] { seqs, viewport.getAlignment().getDataset(), hiddenColumns }; - statusBar.setText("Copied " + seqs.length + " sequences to clipboard."); + statusBar.setText(MessageManager.formatMessage("label.copied_sequences_to_clipboard", new String[]{Integer.valueOf(seqs.length).toString()})); } /** @@ -2299,7 +2296,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.getSelectionGroup()); } - statusBar.setText("Removed " + trimRegion.getSize() + " columns."); + statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()})); addHistoryItem(trimRegion); @@ -2347,8 +2344,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(removeGapCols); - statusBar.setText("Removed " + removeGapCols.getSize() - + " empty columns."); + 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 @@ -2542,7 +2538,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newap.av.viewName = newViewName; addAlignmentPanel(newap, true); - + newap.alignmentChanged(); + if (alignPanels.size() == 2) { viewport.gatherViewsHere = true; @@ -2956,7 +2953,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, editPane.setEditable(false); StringBuffer contents = new AlignmentProperties(viewport.getAlignment()) .formatAsHtml(); - editPane.setText("" + contents.toString() + ""); + editPane.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()})); JInternalFrame frame = new JInternalFrame(); frame.getContentPane().add(new JScrollPane(editPane)); @@ -3416,8 +3413,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int option = JOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, - "Remove from default list?", - "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) { @@ -3569,7 +3566,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, || (viewport.getSelectionGroup().getSize() < 2)) { JOptionPane.showInternalMessageDialog(this, - "You must select at least 2 sequences.", "Invalid Selection", + MessageManager.getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"), JOptionPane.WARNING_MESSAGE); } else @@ -3595,9 +3592,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, || (viewport.getAlignment().getHeight() < 4)) { JOptionPane.showInternalMessageDialog(this, - "Principal component analysis must take\n" - + "at least 4 input sequences.", - "Sequence selection insufficient", + MessageManager.getString("label.principal_component_analysis_must_take_least_four_input_sequences"), + MessageManager.getString("label.sequence_selection_insufficient"), JOptionPane.WARNING_MESSAGE); return; @@ -3699,8 +3695,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - "You need to have more than two sequences selected to build a tree!", - "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; } @@ -3714,10 +3710,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - "The selected region to create a tree may\nonly contain residues or gaps.\n" - + "Try using the Pad function in the edit menu,\n" - + "or one of the multiple sequence alignment web services.", - "Sequences in selection are 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; @@ -3735,10 +3729,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - "The sequences must be aligned before creating a tree.\n" - + "Try using the Pad function in the edit menu,\n" - + "or one of the multiple sequence alignment web services.", - "Sequences not aligned", + MessageManager.getString("label.sequences_must_be_aligned_before_creating_tree"), + MessageManager.getString("label.sequences_not_aligned"), JOptionPane.WARNING_MESSAGE); return; @@ -4052,13 +4044,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { JOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(), - "Problem reading tree file", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.problem_reading_tree_file"), JOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin != null && fin.hasWarningMessage()) { JOptionPane.showMessageDialog(Desktop.desktop, - fin.getWarningMessage(), "Possible problem with tree file", + fin.getWarningMessage(), MessageManager.getString("label.possible_problem_with_tree_file"), JOptionPane.WARNING_MESSAGE); } } @@ -4559,8 +4551,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - "Please select at least three bases in at least one sequence in order to perform a cDNA translation.", - "Translation Failed", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), + MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE); } else { @@ -4593,8 +4585,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - "Unfortunately, something went wrong when translating your sequences.\nPlease take a look in the Jalview java console\nand submit a bug report including the stacktrace.", - "Implementation error: Translation Failed", JOptionPane.ERROR_MESSAGE); + MessageManager.getString("label.error_when_translating_sequences_submit_bug_report"), + MessageManager.getString("label.implementation_error") + MessageManager.getString("translation_failed"), JOptionPane.ERROR_MESSAGE); return; } if (al == null) @@ -4602,8 +4594,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - "Please select at least three bases in at least one sequence in order to perform a cDNA translation.", - "Translation Failed", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"), + MessageManager.getString("label.translation_failed"), JOptionPane.WARNING_MESSAGE); } else { @@ -4802,10 +4794,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, || JOptionPane .showConfirmDialog( this, - "Do you want to automatically associate the " - + filesmatched.size() - + " PDB files with sequences in the alignment that have the same name ?", - "Automatically Associate PDB files by name", + MessageManager.formatMessage("label.automatically_associate_pdb_files_with_sequences_same_name", + new String[]{Integer.valueOf(filesmatched.size()).toString()}), + MessageManager.getString("label.automatically_associate_pdb_files_by_name"), JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) { @@ -4838,10 +4829,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane .showConfirmDialog( this, - "Do you want to ignore the " - + filesnotmatched.size() - + " files whose names did not match any sequence IDs ?", - "Ignore unmatched dropped files ?", + MessageManager.formatMessage("label.ignore_unmatched_dropped_files_info", new String[]{Integer.valueOf(filesnotmatched.size()).toString()}), + MessageManager.getString("label.ignore_unmatched_dropped_files"), JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) { return; @@ -4900,8 +4889,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, tcoffeeColour.setSelected(true); changeColour(new TCoffeeColourScheme(viewport.getAlignment())); isAnnotation = true; - statusBar - .setText("Successfully pasted T-Coffee scores to alignment."); + statusBar.setText(MessageManager.getString("label.successfully_pasted_tcoffee_scores_to_alignment")); } else { @@ -4910,9 +4898,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, JOptionPane .showMessageDialog( Desktop.desktop, - tcf.getWarningMessage() == null ? "Check that the file matches sequence IDs in the alignment." + tcf.getWarningMessage() == null ? MessageManager.getString("label.check_file_matches_sequence_ids_alignment") : tcf.getWarningMessage(), - "Problem reading T-COFFEE score file", + MessageManager.getString("label.problem_reading_tcoffee_score_file"), JOptionPane.WARNING_MESSAGE); } } @@ -5030,7 +5018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (SwingUtilities.isRightMouseButton(e)) { String reply = JOptionPane.showInternalInputDialog(this, - "Enter View Name", "Edit View Name", + MessageManager.getString("label.enter_view_name"), MessageManager.getString("label.enter_view_name"), JOptionPane.QUESTION_MESSAGE); if (reply != null) @@ -5310,7 +5298,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ++i; if (++icomp >= mcomp || i == (otherdb.size())) { - ifetch.setText(imname + " to '" + sname + "'"); + ifetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{imname,sname})); dfetch.add(ifetch); ifetch = new JMenu(); imname = null; @@ -5322,7 +5310,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, ++dbi; if (comp >= mcomp || dbi >= (dbclasses.length)) { - dfetch.setText(mname + " to '" + dbclass + "'"); + dfetch.setText(MessageManager.formatMessage("label.source_to_target",new String[]{mname,dbclass})); rfetch.add(dfetch); dfetch = new JMenu(); mname = null; @@ -5467,6 +5455,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override + protected void createGroup_actionPerformed(ActionEvent e) + { + if (avc.createGroup()) + { + alignPanel.alignmentChanged(); + } + } + + @Override + protected void unGroup_actionPerformed(ActionEvent e) + { + if (avc.unGroup()) + { + alignPanel.alignmentChanged(); + } + } + /** * make the given alignmentPanel the currently selected tab *