From fee1b781ca14aadea5d112fc554fe14879c787c5 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Thu, 24 Nov 2016 16:18:54 +0000 Subject: [PATCH] JAL-2326 updated references of JOptionPane to JvOptionPane --- .../groovy/selectColumnsByFeatureAndGroup.groovy | 4 +- src/MCview/PDBViewer.java | 8 +- src/jalview/gui/AlignExportSettings.java | 6 +- src/jalview/gui/AlignFrame.java | 88 ++++++++++---------- src/jalview/gui/AlignViewport.java | 4 +- src/jalview/gui/AnnotationPanel.java | 4 +- src/jalview/gui/AppJmol.java | 4 +- src/jalview/gui/AppVarnaBinding.java | 4 +- src/jalview/gui/AssociatePdbFileWithSeq.java | 4 +- src/jalview/gui/ChimeraViewFrame.java | 18 ++-- src/jalview/gui/CrossRefAction.java | 4 +- src/jalview/gui/CutAndPasteTransfer.java | 13 ++- src/jalview/gui/DasSourceBrowser.java | 14 ++-- src/jalview/gui/Desktop.java | 48 +++++------ src/jalview/gui/EPSOptions.java | 6 +- src/jalview/gui/EditNameDialog.java | 6 +- src/jalview/gui/FeatureRenderer.java | 14 ++-- src/jalview/gui/FeatureSettings.java | 6 +- src/jalview/gui/Finder.java | 12 +-- src/jalview/gui/FontChooser.java | 4 +- src/jalview/gui/HTMLOptions.java | 6 +- src/jalview/gui/IdPanel.java | 4 +- src/jalview/gui/Jalview2XML.java | 4 +- src/jalview/gui/Jalview2XML_V1.java | 8 +- src/jalview/gui/JvOptionPane.java | 10 --- src/jalview/gui/OOMWarning.java | 6 +- src/jalview/gui/PCAPanel.java | 4 +- src/jalview/gui/PopupMenu.java | 8 +- src/jalview/gui/Preferences.java | 30 +++---- src/jalview/gui/PromptUserConfig.java | 12 +-- src/jalview/gui/RestInputParamEditDialog.java | 8 +- src/jalview/gui/SVGOptions.java | 6 +- src/jalview/gui/SeqPanel.java | 4 +- src/jalview/gui/SequenceFetcher.java | 8 +- src/jalview/gui/StructureChooser.java | 8 +- src/jalview/gui/StructureViewerBase.java | 18 ++-- src/jalview/gui/TextColourChooser.java | 8 +- src/jalview/gui/UserDefinedColours.java | 18 ++-- src/jalview/gui/UserQuestionnaireCheck.java | 8 +- src/jalview/gui/VamsasApplication.java | 12 +-- src/jalview/gui/WebserviceInfo.java | 4 +- src/jalview/gui/WsJobParameters.java | 32 +++++-- src/jalview/gui/WsParamSetManager.java | 4 +- src/jalview/gui/WsPreferences.java | 26 +++--- src/jalview/io/FileLoader.java | 18 ++-- src/jalview/io/JalviewFileChooser.java | 8 +- src/jalview/io/WSWUBlastClient.java | 10 ++- src/jalview/jbgui/GAlignFrame.java | 8 +- src/jalview/jbgui/GSequenceLink.java | 6 +- src/jalview/ws/DasSequenceFeatureFetcher.java | 13 ++- src/jalview/ws/jws1/Discoverer.java | 9 +- src/jalview/ws/jws1/JPredClient.java | 8 +- src/jalview/ws/jws1/MsaWSClient.java | 10 +-- src/jalview/ws/jws1/SeqSearchWSClient.java | 10 +-- src/jalview/ws/jws2/MsaWSClient.java | 14 ++-- .../ws/jws2/SequenceAnnotationWSClient.java | 4 +- src/jalview/ws/rest/RestClient.java | 6 +- 57 files changed, 339 insertions(+), 312 deletions(-) diff --git a/examples/groovy/selectColumnsByFeatureAndGroup.groovy b/examples/groovy/selectColumnsByFeatureAndGroup.groovy index 0b479bf..b8edaa7 100644 --- a/examples/groovy/selectColumnsByFeatureAndGroup.groovy +++ b/examples/groovy/selectColumnsByFeatureAndGroup.groovy @@ -92,8 +92,8 @@ return "Found a total of ${nfeat} features across ${nseq} sequences in ${nal} al String getFeatureInput(){ def swingBuilder = new SwingBuilder(); - def response = JOptionPane.showInputDialog( - null, 'Select columns by feature by type','Enter type of feature', JOptionPane.OK_OPTION) + def response = JvOptionPane.showInputDialog( + null, 'Select columns by feature by type','Enter type of feature', JvOptionPane.OK_OPTION) return response } \ No newline at end of file diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java index eaa33df..d6b05c4 100755 --- a/src/MCview/PDBViewer.java +++ b/src/MCview/PDBViewer.java @@ -24,6 +24,7 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.gui.AlignmentPanel; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.OOMWarning; import jalview.gui.UserDefinedColours; import jalview.io.JalviewFileChooser; @@ -60,7 +61,6 @@ import javax.swing.JInternalFrame; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JRadioButtonMenuItem; public class PDBViewer extends JInternalFrame implements Runnable @@ -436,13 +436,13 @@ public class PDBViewer extends JInternalFrame implements Runnable { radioItem.removeActionListener(radioItem.getActionListeners()[0]); - int option = JOptionPane.showInternalConfirmDialog( + int option = JvOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, MessageManager .getString("label.remove_from_default_list"), MessageManager .getString("label.remove_user_defined_colour"), - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) + JvOptionPane.YES_NO_OPTION); + if (option == JvOptionPane.YES_OPTION) { jalview.gui.UserDefinedColours .removeColourFromDefaults(radioItem.getText()); diff --git a/src/jalview/gui/AlignExportSettings.java b/src/jalview/gui/AlignExportSettings.java index 2a12630..a4fdd7d 100644 --- a/src/jalview/gui/AlignExportSettings.java +++ b/src/jalview/gui/AlignExportSettings.java @@ -48,11 +48,12 @@ public class AlignExportSettings extends GAlignExportSettings implements { JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION, - JOptionPane.DEFAULT_OPTION, null, new Object[] { this }); + JvOptionPane.DEFAULT_OPTION, null, new Object[] { this }); dialog = pane.createDialog(Desktop.desktop, MessageManager.getString("label.export_settings")); dialog.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { cancelled = true; @@ -66,6 +67,7 @@ public class AlignExportSettings extends GAlignExportSettings implements } } + @Override public void ok_actionPerformed(ActionEvent e) { cancelled = false; @@ -73,6 +75,7 @@ public class AlignExportSettings extends GAlignExportSettings implements dialog.dispose(); } + @Override public void cancel_actionPerformed(ActionEvent e) { cancelled = true; @@ -110,6 +113,7 @@ public class AlignExportSettings extends GAlignExportSettings implements return chkExportGrps.isSelected(); } + @Override public boolean isCancelled() { return cancelled; diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 6a637e3..7b751bf 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1128,14 +1128,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, currentFileFormat = chooser.getSelectedFormat(); while (currentFileFormat == null) { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager .getString("label.select_file_format_before_saving"), MessageManager .getString("label.file_format_not_specified"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); currentFileFormat = chooser.getSelectedFormat(); value = chooser.showSaveDialog(this); if (value != JalviewFileChooser.APPROVE_OPTION) @@ -1236,11 +1236,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!success) { - JOptionPane.showInternalMessageDialog(this, MessageManager + JvOptionPane.showInternalMessageDialog(this, MessageManager .formatMessage("label.couldnt_save_file", new Object[] { fileName }), MessageManager .getString("label.error_saving_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } return success; @@ -1255,8 +1255,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - JOptionPane.showInternalMessageDialog(this, warning, title, - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(this, warning, title, + JvOptionPane.WARNING_MESSAGE); } return; } @@ -2368,13 +2368,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getAlignment().getWidth()) ? true : false; if (isEntireAlignWidth) { - int confirm = JOptionPane.showConfirmDialog(this, + int confirm = JvOptionPane.showConfirmDialog(this, MessageManager.getString("warn.delete_all"), // $NON-NLS-1$ MessageManager.getString("label.delete_all"), // $NON-NLS-1$ - JOptionPane.OK_CANCEL_OPTION); + JvOptionPane.OK_CANCEL_OPTION); - if (confirm == JOptionPane.CANCEL_OPTION - || confirm == JOptionPane.CLOSED_OPTION) + if (confirm == JvOptionPane.CANCEL_OPTION + || confirm == JvOptionPane.CLOSED_OPTION) { return; } @@ -3651,13 +3651,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { radioItem.removeActionListener(radioItem.getActionListeners()[0]); - int option = JOptionPane.showInternalConfirmDialog( + int option = JvOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, MessageManager .getString("label.remove_from_default_list"), MessageManager .getString("label.remove_user_defined_colour"), - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) + JvOptionPane.YES_NO_OPTION); + if (option == JvOptionPane.YES_OPTION) { jalview.gui.UserDefinedColours .removeColourFromDefaults(radioItem.getText()); @@ -3805,10 +3805,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if ((viewport.getSelectionGroup() == null) || (viewport.getSelectionGroup().getSize() < 2)) { - JOptionPane.showInternalMessageDialog(this, MessageManager + JvOptionPane.showInternalMessageDialog(this, MessageManager .getString("label.you_must_select_least_two_sequences"), MessageManager.getString("label.invalid_selection"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } else { @@ -3834,14 +3834,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getSelectionGroup().getSize() > 0)) || (viewport.getAlignment().getHeight() < 4)) { - JOptionPane + JvOptionPane .showInternalMessageDialog( this, MessageManager .getString("label.principal_component_analysis_must_take_least_four_input_sequences"), MessageManager .getString("label.sequence_selection_insufficient"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -3939,14 +3939,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (viewport.getSelectionGroup().getSize() < 3) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.you_need_more_two_sequences_selected_build_tree"), MessageManager .getString("label.not_enough_sequences"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -3957,14 +3957,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (_s.getLength() < sg.getEndRes()) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.selected_region_to_tree_may_only_contain_residues_or_gaps"), MessageManager .getString("label.sequences_selection_not_aligned"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -3978,14 +3978,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // are the visible sequences aligned? if (!viewport.getAlignment().isAligned(false)) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, MessageManager .getString("label.sequences_must_be_aligned_before_creating_tree"), MessageManager .getString("label.sequences_not_aligned"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -4250,11 +4250,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() == 1) { - int option = JOptionPane.showConfirmDialog(this, + int option = JvOptionPane.showConfirmDialog(this, MessageManager.getString("warn.oneseq_msainput_selection"), MessageManager.getString("label.invalid_selection"), - JOptionPane.OK_CANCEL_OPTION); - if (option == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION); + if (option == JvOptionPane.OK_OPTION) { msa = viewport.getAlignmentView(false); } @@ -4330,21 +4330,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, ex.getMessage(), MessageManager .getString("label.problem_reading_tree_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } if (fin != null && fin.hasWarningMessage()) { - JOptionPane.showMessageDialog(Desktop.desktop, fin + JvOptionPane.showMessageDialog(Desktop.desktop, fin .getWarningMessage(), MessageManager .getString("label.possible_problem_with_tree_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } } @@ -4729,8 +4729,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final String errorTitle = MessageManager .getString("label.implementation_error") + MessageManager.getString("label.translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JOptionPane.ERROR_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JvOptionPane.ERROR_MESSAGE); return; } if (al == null || al.getHeight() == 0) @@ -4739,8 +4739,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation"); final String errorTitle = MessageManager .getString("label.translation_failed"); - JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle, + JvOptionPane.WARNING_MESSAGE); } else { @@ -4911,7 +4911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (filesmatched.size() > 0) { if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JOptionPane + || JvOptionPane .showConfirmDialog( this, MessageManager @@ -4924,7 +4924,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .toString() }), MessageManager .getString("label.automatically_associate_structure_files_by_name"), - JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION) + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION) { for (Object[] fm : filesmatched) @@ -4954,7 +4954,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (assocfiles > 0 && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane .showConfirmDialog( this, "" @@ -4969,7 +4969,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + "", MessageManager .getString("label.ignore_unmatched_dropped_files"), - JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION)) + JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION)) { return; } @@ -5034,7 +5034,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { // some problem - if no warning its probable that the ID matching // process didn't work - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, tcf.getWarningMessage() == null ? MessageManager @@ -5042,7 +5042,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, : tcf.getWarningMessage(), MessageManager .getString("label.problem_reading_tcoffee_score_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } else @@ -5163,8 +5163,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (e.isPopupTrigger()) { String msg = MessageManager.getString("label.enter_view_name"); - String reply = JOptionPane.showInternalInputDialog(this, msg, msg, - JOptionPane.QUESTION_MESSAGE); + String reply = JvOptionPane.showInternalInputDialog(this, msg, msg, + JvOptionPane.QUESTION_MESSAGE); if (reply != null) { @@ -5903,12 +5903,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } catch (Exception ex) { System.err.println((ex.toString())); - JOptionPane + JvOptionPane .showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.couldnt_run_groovy_script"), MessageManager .getString("label.groovy_support_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } else diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 03aee5d..39217e5 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -876,9 +876,9 @@ public class AlignViewport extends AlignmentViewport implements MessageManager.getString("label.new_window"), }; final String question = JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.open_split_window?")); - int response = JOptionPane.showOptionDialog(Desktop.desktop, question, + int response = JvOptionPane.showOptionDialog(Desktop.desktop, question, MessageManager.getString("label.open_split_window"), - JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null, + JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); if (response != 1 && response != 2) diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 199c4e5..b1f0edb 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -300,7 +300,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, else if (action.equals(LABEL)) { String exMesg = collectAnnotVals(anot, LABEL); - String label = JOptionPane.showInputDialog(this, + String label = JvOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"), exMesg); if (label == null) @@ -380,7 +380,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, aa[activeRow].hasIcons = true; } - String label = JOptionPane.showInputDialog(MessageManager + String label = JvOptionPane.showInputDialog(MessageManager .getString("label.enter_label_for_the_structure"), symbol); if (label == null) diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index d7e8305..e2e54aa 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -675,11 +675,11 @@ public class AppJmol extends StructureViewerBase } if (errormsgs.length() > 0) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[] { errormsgs.toString() }), MessageManager.getString("label.couldnt_load_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } return files; } diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java index 521bb3e..8ab1e61 100644 --- a/src/jalview/gui/AppVarnaBinding.java +++ b/src/jalview/gui/AppVarnaBinding.java @@ -374,9 +374,9 @@ public class AppVarnaBinding extends JalviewVarnaBinding _sideList.ensureIndexIsVisible(index); /* - * TODO Object newName = JOptionPane.showInputDialog( this, + * TODO Object newName = JvOptionPane.showInputDialog( this, * "Specify a new name for this RNA", "Rename RNA", - * JOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if + * JvOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if * (newName!=null) { item.name = newName.toString(); * this._sideList.repaint(); } */ diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java index e2637a9..f0cee7c 100644 --- a/src/jalview/gui/AssociatePdbFileWithSeq.java +++ b/src/jalview/gui/AssociatePdbFileWithSeq.java @@ -64,11 +64,11 @@ public class AssociatePdbFileWithSeq if (prompt) { - reply = JOptionPane.showInternalInputDialog(Desktop.desktop, + reply = JvOptionPane.showInternalInputDialog(Desktop.desktop, MessageManager .getString("label.couldnt_find_pdb_id_in_file"), MessageManager.getString("label.no_pdb_id_in_file"), - JOptionPane.QUESTION_MESSAGE); + JvOptionPane.QUESTION_MESSAGE); } if (reply == null) { diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index fe12f40..90ad51d 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -377,10 +377,10 @@ public class ChimeraViewFrame extends StructureViewerBase if (!jmb.launchChimera()) { - JOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager.getString("label.chimera_failed"), MessageManager.getString("label.error_loading_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); this.dispose(); return; } @@ -441,18 +441,18 @@ public class ChimeraViewFrame extends StructureViewerBase "label.confirm_close_chimera", new Object[] { jmb.getViewerTitle("Chimera", false) }); prompt = JvSwingUtils.wrapTooltip(true, prompt); - int confirm = JOptionPane.showConfirmDialog(this, prompt, + int confirm = JvOptionPane.showConfirmDialog(this, prompt, MessageManager.getString("label.close_viewer"), - JOptionPane.YES_NO_CANCEL_OPTION); + JvOptionPane.YES_NO_CANCEL_OPTION); /* * abort closure if user hits escape or Cancel */ - if (confirm == JOptionPane.CANCEL_OPTION - || confirm == JOptionPane.CLOSED_OPTION) + if (confirm == JvOptionPane.CANCEL_OPTION + || confirm == JvOptionPane.CLOSED_OPTION) { return; } - closeChimera = confirm == JOptionPane.YES_OPTION; + closeChimera = confirm == JvOptionPane.YES_OPTION; } jmb.closeViewer(closeChimera); } @@ -541,11 +541,11 @@ public class ChimeraViewFrame extends StructureViewerBase if (errormsgs.length() > 0) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", new Object[] { errormsgs.toString() }), MessageManager.getString("label.couldnt_load_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } if (files.length() > 0) diff --git a/src/jalview/gui/CrossRefAction.java b/src/jalview/gui/CrossRefAction.java index 32af226..7768b22 100644 --- a/src/jalview/gui/CrossRefAction.java +++ b/src/jalview/gui/CrossRefAction.java @@ -121,10 +121,10 @@ public class CrossRefAction implements Runnable xrefsAlignment.getSequencesArray()); if (copyAlignment.getHeight() == 0) { - JOptionPane.showMessageDialog(alignFrame, + JvOptionPane.showMessageDialog(alignFrame, MessageManager.getString("label.cant_map_cds"), MessageManager.getString("label.operation_failed"), - JOptionPane.OK_OPTION); + JvOptionPane.OK_OPTION); System.err.println("Failed to make CDS alignment"); } diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index ed2b9bf..4184eca 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -51,7 +51,6 @@ import java.awt.event.ActionListener; import java.awt.event.MouseEvent; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; @@ -220,10 +219,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer .getString("label.couldnt_read_data")); if (!Jalview.isHeadlessMode()) { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, AppletFormatAdapter.SUPPORTED_FORMATS, MessageManager.getString("label.couldnt_read_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } return; } @@ -241,12 +240,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer } catch (java.io.IOException ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage( "label.couldnt_read_pasted_text", new String[] { ex.toString() }), MessageManager .getString("label.error_parsing_text"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } @@ -330,10 +329,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer .getString("label.couldnt_read_data")); if (!Jalview.isHeadlessMode()) { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, AppletFormatAdapter.SUPPORTED_FORMATS, MessageManager.getString("label.couldnt_read_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } } diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java index e677084..8c8f228 100644 --- a/src/jalview/gui/DasSourceBrowser.java +++ b/src/jalview/gui/DasSourceBrowser.java @@ -459,12 +459,12 @@ public class DasSourceBrowser extends GDasSourceBrowser implements pane12.add(urltf, BorderLayout.EAST); panel.add(pane12, BorderLayout.SOUTH); - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, panel, MessageManager.getString("label.enter_local_das_source"), - JOptionPane.OK_CANCEL_OPTION); + JvOptionPane.OK_CANCEL_OPTION); - if (reply != JOptionPane.OK_OPTION) + if (reply != JvOptionPane.OK_OPTION) { return; } @@ -534,21 +534,21 @@ public class DasSourceBrowser extends GDasSourceBrowser implements if (!sourceRegistry.getSource(nickname).isLocal()) { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager .getString("label.you_can_only_edit_or_remove_local_das_sources"), MessageManager.getString("label.public_das_source"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } Object[] options = { "Edit", "Remove", "Cancel" }; - int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop, + int choice = JvOptionPane.showInternalOptionDialog(Desktop.desktop, "Do you want to edit or remove " + nickname + "?", "Edit / Remove Local DAS Source", - JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, + JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.QUESTION_MESSAGE, null, options, options[2]); switch (choice) diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 28606f1..6dd7557 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1086,11 +1086,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } } - int reply = JOptionPane.showInternalConfirmDialog(desktop, panel, + int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel, MessageManager.getString("label.input_alignment_from_url"), - JOptionPane.OK_CANCEL_OPTION); + JvOptionPane.OK_CANCEL_OPTION); - if (reply != JOptionPane.OK_OPTION) + if (reply != JvOptionPane.OK_OPTION) { return; } @@ -1115,11 +1115,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements if (format.equals("URL NOT FOUND")) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", new Object[] { url }), MessageManager .getString("label.url_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -1214,9 +1214,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements public void aboutMenuItem_actionPerformed(ActionEvent e) { // StringBuffer message = getAboutMessage(false); - // JOptionPane.showInternalMessageDialog(Desktop.desktop, + // JvOptionPane.showInternalMessageDialog(Desktop.desktop, // - // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE); + // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE); new Thread(new Runnable() { @Override @@ -1556,11 +1556,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements Cache.log.error( "Problems whilst trying to save to " + choice.getName(), ex); - JOptionPane.showMessageDialog(me, MessageManager.formatMessage( + JvOptionPane.showMessageDialog(me, MessageManager.formatMessage( "label.error_whilst_saving_current_state_to", new Object[] { choice.getName() }), MessageManager .getString("label.couldnt_save_project"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } @@ -1622,12 +1622,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements { Cache.log.error("Problems whilst loading project from " + choice, ex); - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage( "label.error_whilst_loading_project_from", new Object[] { choice }), MessageManager .getString("label.couldnt_load_project"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } setProgressBar(null, choice.hashCode()); } @@ -1912,7 +1912,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements String fle = chooser.getSelectedFile().toString(); if (!vamsasImport(chooser.getSelectedFile())) { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( @@ -1920,7 +1920,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements new Object[] { fle }), MessageManager .getString("label.vamsas_document_import_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } } @@ -2212,9 +2212,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements removeProgressPanel(progpanel); if (warnmsg != null) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, - warnmsg, warnttl, JOptionPane.ERROR_MESSAGE); + warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE); } } } @@ -2334,10 +2334,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); msgPanel.add(jcb); - JOptionPane.showMessageDialog(Desktop.desktop, msgPanel, + JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel, MessageManager .getString("label.SEQUENCE_ID_no_longer_used"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } }); @@ -2544,11 +2544,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements } catch (Exception ex) { jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex); - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_create_groovy_shell"), MessageManager.getString("label.groovy_support_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } @@ -2889,7 +2889,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements * * jd.waitForInput(); */ - JOptionPane + JvOptionPane .showConfirmDialog( Desktop.desktop, new JLabel( @@ -2901,8 +2901,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements + "

Check the Connections and Web services tab
of the" + " Tools->Preferences dialog box to change them.

"), "Web Service Configuration Problem", - JOptionPane.DEFAULT_OPTION, - JOptionPane.ERROR_MESSAGE); + JvOptionPane.DEFAULT_OPTION, + JvOptionPane.ERROR_MESSAGE); serviceChangedDialog = null; } @@ -2959,11 +2959,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } diff --git a/src/jalview/gui/EPSOptions.java b/src/jalview/gui/EPSOptions.java index 69fde89..fa67999 100644 --- a/src/jalview/gui/EPSOptions.java +++ b/src/jalview/gui/EPSOptions.java @@ -58,8 +58,8 @@ public class EPSOptions extends JPanel bg.add(lineart); bg.add(text); - JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION, - JOptionPane.DEFAULT_OPTION, null, new Object[] { this }); + JOptionPane pane = new JOptionPane(null, JvOptionPane.DEFAULT_OPTION, + JvOptionPane.DEFAULT_OPTION, null, new Object[] { this }); dialog = pane.createDialog(Desktop.desktop, "EPS Rendering options"); dialog.setVisible(true); @@ -78,6 +78,7 @@ public class EPSOptions extends JPanel ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ok_actionPerformed(e); @@ -86,6 +87,7 @@ public class EPSOptions extends JPanel cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cancel_actionPerformed(e); diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java index baad794..0ec4a87 100644 --- a/src/jalview/gui/EditNameDialog.java +++ b/src/jalview/gui/EditNameDialog.java @@ -80,13 +80,13 @@ public class EditNameDialog panel2.add(description, BorderLayout.CENTER); panel.add(panel2, BorderLayout.SOUTH); } - int reply = JOptionPane.showInternalConfirmDialog(parent, panel, title, - JOptionPane.OK_CANCEL_OPTION); + int reply = JvOptionPane.showInternalConfirmDialog(parent, panel, title, + JvOptionPane.OK_CANCEL_OPTION); if (!parent.requestFocusInWindow()) { System.err.println("Bad focus for dialog!"); } - if (reply == JOptionPane.OK_OPTION) + if (reply == JvOptionPane.OK_OPTION) { accept = true; } diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java index 83d1612..ae911ed 100644 --- a/src/jalview/gui/FeatureRenderer.java +++ b/src/jalview/gui/FeatureRenderer.java @@ -330,14 +330,14 @@ public class FeatureRenderer extends : MessageManager.formatMessage("label.amend_delete_features", new String[] { sequences[0].getName() }); - int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, - bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION, - JOptionPane.QUESTION_MESSAGE, null, options, + int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop, + bigPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION, + JvOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok")); jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile(); - if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0) + if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0) { // This ensures that the last sequence // is refreshed and new features are rendered @@ -356,11 +356,11 @@ public class FeatureRenderer extends { SequenceFeature sf = features[featureIndex]; - if (reply == JOptionPane.NO_OPTION) + if (reply == JvOptionPane.NO_OPTION) { sequences[0].getDatasetSequence().deleteFeature(sf); } - else if (reply == JOptionPane.YES_OPTION) + else if (reply == JvOptionPane.YES_OPTION) { sf.type = lastFeatureAdded; sf.featureGroup = lastFeatureGroupAdded; @@ -383,7 +383,7 @@ public class FeatureRenderer extends else // NEW FEATURES ADDED { - if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) + if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0) { for (int i = 0; i < sequences.length; i++) { diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java index 15f3e5b..e3cdf76 100644 --- a/src/jalview/gui/FeatureSettings.java +++ b/src/jalview/gui/FeatureSettings.java @@ -1402,15 +1402,15 @@ public class FeatureSettings extends JPanel implements public void noDasSourceActive() { complete(); - JOptionPane + JvOptionPane .showInternalConfirmDialog( Desktop.desktop, MessageManager .getString("label.no_das_sources_selected_warn"), MessageManager .getString("label.no_das_sources_selected_title"), - JOptionPane.DEFAULT_OPTION, - JOptionPane.INFORMATION_MESSAGE); + JvOptionPane.DEFAULT_OPTION, + JvOptionPane.INFORMATION_MESSAGE); } // /////////////////////////////////////////////////////////////////////// diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index a8dbc38..af23ceb 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -293,9 +293,9 @@ public class Finder extends GFinder // 'SelectRegion' selection if (!haveResults) { - JOptionPane.showInternalMessageDialog(this, + JvOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"), null, - JOptionPane.INFORMATION_MESSAGE); + JvOptionPane.INFORMATION_MESSAGE); resIndex = -1; seqIndex = 0; } @@ -315,8 +315,8 @@ public class Finder extends GFinder message += searchResults.getSize() + " subsequence matches found."; } - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); + JvOptionPane.showInternalMessageDialog(this, message, null, + JvOptionPane.INFORMATION_MESSAGE); resIndex = -1; seqIndex = 0; } @@ -338,9 +338,9 @@ public class Finder extends GFinder { return false; } - JOptionPane.showInternalMessageDialog(this, error, + JvOptionPane.showInternalMessageDialog(this, error, MessageManager.getString("label.invalid_search"), // $NON-NLS-1$ - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); return true; } diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java index 1f6c068..8220aea 100755 --- a/src/jalview/gui/FontChooser.java +++ b/src/jalview/gui/FontChooser.java @@ -253,9 +253,9 @@ public class FontChooser extends GFontChooser String message = iBounds.getHeight() < 1 ? MessageManager .getString("label.font_doesnt_have_letters_defined") : MessageManager.getString("label.font_too_small"); - JOptionPane.showInternalMessageDialog(this, message, + JvOptionPane.showInternalMessageDialog(this, message, MessageManager.getString("label.invalid_font"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); /* * Restore the changed value - note this will reinvoke this method via the * ActionListener, but now validation should pass diff --git a/src/jalview/gui/HTMLOptions.java b/src/jalview/gui/HTMLOptions.java index 108080b..12af734 100644 --- a/src/jalview/gui/HTMLOptions.java +++ b/src/jalview/gui/HTMLOptions.java @@ -58,8 +58,8 @@ public class HTMLOptions extends JPanel bg.add(lineart); bg.add(text); - JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION, - JOptionPane.DEFAULT_OPTION, null, new Object[] { this }); + JOptionPane pane = new JOptionPane(null, JvOptionPane.DEFAULT_OPTION, + JvOptionPane.DEFAULT_OPTION, null, new Object[] { this }); dialog = pane.createDialog(Desktop.desktop, "HTML Rendering options"); dialog.setVisible(true); @@ -78,6 +78,7 @@ public class HTMLOptions extends JPanel ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ok_actionPerformed(e); @@ -86,6 +87,7 @@ public class HTMLOptions extends JPanel cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cancel_actionPerformed(e); diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 6a20872..59d12d9 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -254,10 +254,10 @@ public class IdPanel extends JPanel implements MouseListener, jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } } diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index bc5e1d8..00c32e9 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -2636,10 +2636,10 @@ public class Jalview2XML @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, finalErrorMessage, "Error " + (saving ? "saving" : "loading") - + " Jalview file", JOptionPane.WARNING_MESSAGE); + + " Jalview file", JvOptionPane.WARNING_MESSAGE); } }); } diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java index 3b39be7..2e6706c 100755 --- a/src/jalview/gui/Jalview2XML_V1.java +++ b/src/jalview/gui/Jalview2XML_V1.java @@ -155,11 +155,11 @@ public class Jalview2XML_V1 System.err.println("Couldn't locate Jalview XML file : " + ex + "\n"); - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage("label.couldnt_locate", new String[] { file }), MessageManager .getString("label.url_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -176,12 +176,12 @@ public class Jalview2XML_V1 public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.formatMessage( "label.error_loading_file_params", new String[] { file }), MessageManager .getString("label.error_loading_jalview_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } diff --git a/src/jalview/gui/JvOptionPane.java b/src/jalview/gui/JvOptionPane.java index a6192be..539f3c2 100644 --- a/src/jalview/gui/JvOptionPane.java +++ b/src/jalview/gui/JvOptionPane.java @@ -272,16 +272,6 @@ public class JvOptionPane extends JOptionPane .toString(); } - // (mockResponse != DONT_MOCK) ? mockResponse : - // if (isMockMode()) - // { - // - // } - // else - // { - // JOptionPane - // } - private static void outputMessage(Object message) { System.out.println(">>> JOption Message : " + message.toString()); diff --git a/src/jalview/gui/OOMWarning.java b/src/jalview/gui/OOMWarning.java index eb4425e..f519b85 100644 --- a/src/jalview/gui/OOMWarning.java +++ b/src/jalview/gui/OOMWarning.java @@ -75,13 +75,15 @@ public class OOMWarning implements Runnable this(string, oomerror, Desktop.desktop); } + @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog(desktop, + JvOptionPane + .showInternalMessageDialog(desktop, MessageManager.formatMessage("warn.out_of_memory_when_action", new String[] { action }), MessageManager .getString("label.out_of_memory"), - javax.swing.JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); // hope that there's enough memory left that no more appear. oomInprogress = false; } diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 51d247d..4f5a018 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -114,10 +114,10 @@ public class PCAPanel extends GPCAPanel implements Runnable, if (!sameLength) { - JOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager.getString("label.pca_sequences_not_aligned"), MessageManager.getString("label.sequences_not_aligned"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 5825382..cf010dc 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -2088,14 +2088,14 @@ public class PopupMenu extends JPopupMenu { if (dialog.getName().indexOf(" ") > -1) { - JOptionPane + JvOptionPane .showMessageDialog( ap, MessageManager .getString("label.spaces_converted_to_backslashes"), MessageManager .getString("label.no_spaces_allowed_sequence_name"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } sequence.setName(dialog.getName().replace(' ', '_')); @@ -2194,10 +2194,10 @@ public class PopupMenu extends JPopupMenu jalview.util.BrowserLauncher.openURL(url); } catch (Exception ex) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.web_browser_not_found_unix"), MessageManager.getString("label.web_browser_not_found"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); ex.printStackTrace(); } diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 3bffd3a..b293e6f 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -754,9 +754,9 @@ public class Preferences extends GPreferences boolean valid = false; while (!valid) { - if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, MessageManager.getString("label.new_sequence_url_link"), - JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { @@ -781,10 +781,10 @@ public class Preferences extends GPreferences int index = linkNameList.getSelectedIndex(); if (index == -1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -795,9 +795,9 @@ public class Preferences extends GPreferences while (!valid) { - if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link, + if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, MessageManager.getString("label.new_sequence_url_link"), - JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { @@ -821,10 +821,10 @@ public class Preferences extends GPreferences int index = linkNameList.getSelectedIndex(); if (index == -1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } nameLinks.removeElementAt(index); @@ -916,10 +916,10 @@ public class Preferences extends GPreferences } } catch (NumberFormatException x) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("warn.user_defined_width_requirements"), MessageManager.getString("label.invalid_id_column_width"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); userIdWidth.setText(""); } } @@ -942,10 +942,10 @@ public class Preferences extends GPreferences File f = new File(chimeraPath.getText()); if (!f.canExecute()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.invalid_chimera_path"), MessageManager.getString("label.invalid_name"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); return false; } } @@ -981,13 +981,13 @@ public class Preferences extends GPreferences if (!found) { String[] options = { "OK", "Help" }; - int showHelp = JOptionPane.showInternalOptionDialog( + int showHelp = JvOptionPane.showInternalOptionDialog( Desktop.desktop, JvSwingUtils.wrapTooltip(true, MessageManager.getString("label.chimera_missing")), - "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE, + "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE, null, options, options[0]); - if (showHelp == JOptionPane.NO_OPTION) + if (showHelp == JvOptionPane.NO_OPTION) { try { diff --git a/src/jalview/gui/PromptUserConfig.java b/src/jalview/gui/PromptUserConfig.java index d7449d0..fb90ce7 100644 --- a/src/jalview/gui/PromptUserConfig.java +++ b/src/jalview/gui/PromptUserConfig.java @@ -201,12 +201,12 @@ public class PromptUserConfig implements Runnable } try { - int reply = JOptionPane.showConfirmDialog( + int reply = JvOptionPane.showConfirmDialog( Desktop.desktop, // component, dialogText, dialogTitle, - (allowCancel) ? JOptionPane.YES_NO_CANCEL_OPTION - : JOptionPane.YES_NO_OPTION, - JOptionPane.QUESTION_MESSAGE); + (allowCancel) ? JvOptionPane.YES_NO_CANCEL_OPTION + : JvOptionPane.YES_NO_OPTION, + JvOptionPane.QUESTION_MESSAGE); // now, ask the desktop to relayer any external windows that might have // been obsured if (Desktop.instance != null) @@ -215,11 +215,11 @@ public class PromptUserConfig implements Runnable } // and finish parsing the result jalview.bin.Cache.log.debug("Got response : " + reply); - if (reply == JOptionPane.YES_OPTION) + if (reply == JvOptionPane.YES_OPTION) { jalview.bin.Cache.setProperty(property, "true"); } - else if (reply == JOptionPane.NO_OPTION) + else if (reply == JvOptionPane.NO_OPTION) { if (removeifunset) { diff --git a/src/jalview/gui/RestInputParamEditDialog.java b/src/jalview/gui/RestInputParamEditDialog.java index 8056189..19a9b51 100644 --- a/src/jalview/gui/RestInputParamEditDialog.java +++ b/src/jalview/gui/RestInputParamEditDialog.java @@ -74,13 +74,13 @@ public class RestInputParamEditDialog extends GRestInputParamEditDialog @Override protected void okPressed() { - reply = JOptionPane.OK_OPTION; + reply = JvOptionPane.OK_OPTION; } @Override protected void cancelPressed() { - reply = JOptionPane.CANCEL_OPTION; + reply = JvOptionPane.CANCEL_OPTION; } }; @@ -107,14 +107,14 @@ public class RestInputParamEditDialog extends GRestInputParamEditDialog + currentservice.getName(), 600, 800); initTypeLists(); - reply = JOptionPane.CANCEL_OPTION; + reply = JvOptionPane.CANCEL_OPTION; old = toedit; current = null; if (old != null) { setStateFor(old); } - updated = updated && reply == JOptionPane.OK_OPTION; + updated = updated && reply == JvOptionPane.OK_OPTION; frame.validate(); } diff --git a/src/jalview/gui/SVGOptions.java b/src/jalview/gui/SVGOptions.java index a64819a..ea8e360 100644 --- a/src/jalview/gui/SVGOptions.java +++ b/src/jalview/gui/SVGOptions.java @@ -58,8 +58,8 @@ public class SVGOptions extends JPanel bg.add(lineart); bg.add(text); - JOptionPane pane = new JOptionPane(null, JOptionPane.DEFAULT_OPTION, - JOptionPane.DEFAULT_OPTION, null, new Object[] { this }); + JOptionPane pane = new JOptionPane(null, JvOptionPane.DEFAULT_OPTION, + JvOptionPane.DEFAULT_OPTION, null, new Object[] { this }); dialog = pane.createDialog(Desktop.desktop, "SVG Rendering options"); dialog.setVisible(true); @@ -78,6 +78,7 @@ public class SVGOptions extends JPanel ok.setText(MessageManager.getString("action.ok")); ok.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { ok_actionPerformed(e); @@ -86,6 +87,7 @@ public class SVGOptions extends JPanel cancel.setText(MessageManager.getString("action.cancel")); cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { cancel_actionPerformed(e); diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 36fb052..8726c4a 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1566,10 +1566,10 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.cannot_edit_annotations_in_wrapped_view"), MessageManager.getString("label.wrapped_view_no_edit"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index bbe2f68..d5fa86d 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -234,14 +234,14 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void run() { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager .getString("warn.couldnt_create_sequence_fetcher_client"), MessageManager .getString("label.couldnt_create_sequence_fetcher"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } }); @@ -1059,9 +1059,9 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, error, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, error, MessageManager.getString("label.error_retrieving_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 21b6e4f..0c3aa2a 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -216,9 +216,9 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog(this, errorMsg.toString(), + JvOptionPane.showMessageDialog(this, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } } @@ -484,11 +484,11 @@ public class StructureChooser extends GStructureChooser implements { errorMsg.append(error).append("\n"); } - JOptionPane.showMessageDialog( + JvOptionPane.showMessageDialog( null, errorMsg.toString(), MessageManager.getString("label.pdb_web-service_error"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index 4715e48..a23b45f 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -336,17 +336,17 @@ public abstract class StructureViewerBase extends GStructureViewer * * @param pdbId * @param view - * @return YES, NO or CANCEL JOptionPane code + * @return YES, NO or CANCEL JvOptionPane code */ protected int chooseAlignStructureToViewer(String pdbId, StructureViewerBase view) { - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, MessageManager.formatMessage("label.add_pdbentry_to_view", new Object[] { pdbId, view.getTitle() }), MessageManager .getString("label.align_to_existing_structure_view"), - JOptionPane.YES_NO_CANCEL_OPTION); + JvOptionPane.YES_NO_CANCEL_OPTION); return option; } @@ -381,11 +381,11 @@ public abstract class StructureViewerBase extends GStructureViewer continue; } int option = chooseAlignStructureToViewer(pdbId, view); - if (option == JOptionPane.CANCEL_OPTION) + if (option == JvOptionPane.CANCEL_OPTION) { return true; } - else if (option == JOptionPane.YES_OPTION) + else if (option == JvOptionPane.YES_OPTION) { view.useAlignmentPanelForSuperposition(apanel); view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame); @@ -481,19 +481,19 @@ public abstract class StructureViewerBase extends GStructureViewer /* * the PDB file is already loaded */ - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, MessageManager.formatMessage( "label.pdb_entry_is_already_displayed", new Object[] { pdbId }), MessageManager .formatMessage( "label.map_sequences_to_visible_window", new Object[] { pdbId }), - JOptionPane.YES_NO_CANCEL_OPTION); - if (option == JOptionPane.CANCEL_OPTION) + JvOptionPane.YES_NO_CANCEL_OPTION); + if (option == JvOptionPane.CANCEL_OPTION) { finished = true; } - else if (option == JOptionPane.YES_OPTION) + else if (option == JvOptionPane.YES_OPTION) { addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped); finished = true; diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java index 39d9c1d..49fdaf7 100644 --- a/src/jalview/gui/TextColourChooser.java +++ b/src/jalview/gui/TextColourChooser.java @@ -128,16 +128,16 @@ public class TextColourChooser } }); - int reply = JOptionPane + int reply = JvOptionPane .showInternalOptionDialog( ap, bigpanel, MessageManager .getString("label.adjunst_foreground_text_colour_threshold"), - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.QUESTION_MESSAGE, null, null, null); + JvOptionPane.OK_CANCEL_OPTION, + JvOptionPane.QUESTION_MESSAGE, null, null, null); - if (reply == JOptionPane.CANCEL_OPTION) + if (reply == JvOptionPane.CANCEL_OPTION) { if (sg == null) { diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index c9c1531..02470d6 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -456,10 +456,10 @@ public class UserDefinedColours extends GUserDefinedColours implements { if (isNoSelectionMade()) { - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .getString("label.no_colour_selection_in_scheme"), MessageManager.getString("label.no_colour_selection_warn"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } else { @@ -502,10 +502,10 @@ public class UserDefinedColours extends GUserDefinedColours implements { if (isNoSelectionMade()) { - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .getString("label.no_colour_selection_in_scheme"), MessageManager.getString("label.no_colour_selection_warn"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } UserColourScheme ucs = getSchemeFromButtons(); @@ -809,23 +809,23 @@ public class UserDefinedColours extends GUserDefinedColours implements { if (schemeName.getText().trim().length() < 1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.user_colour_scheme_must_have_name"), MessageManager.getString("label.no_name_colour_scheme"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } if (userColourSchemes != null && userColourSchemes.containsKey(schemeName.getText())) { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, MessageManager.formatMessage( "label.colour_scheme_exists_overwrite", new Object[] { schemeName.getText(), schemeName.getText() }), MessageManager.getString("label.duplicate_scheme_name"), - JOptionPane.YES_NO_OPTION); - if (reply != JOptionPane.YES_OPTION) + JvOptionPane.YES_NO_OPTION); + if (reply != JvOptionPane.YES_OPTION) { return; } diff --git a/src/jalview/gui/UserQuestionnaireCheck.java b/src/jalview/gui/UserQuestionnaireCheck.java index eb38ee6..5e5d965 100644 --- a/src/jalview/gui/UserQuestionnaireCheck.java +++ b/src/jalview/gui/UserQuestionnaireCheck.java @@ -142,15 +142,15 @@ public class UserQuestionnaireCheck implements Runnable + qid + "&rid=" + rid; jalview.bin.Cache.log.info("Prompting user for questionnaire at " + qurl); - int reply = JOptionPane + int reply = JvOptionPane .showInternalConfirmDialog(Desktop.desktop, MessageManager .getString("label.jalview_new_questionnaire"), MessageManager .getString("label.jalview_user_survey"), - JOptionPane.YES_NO_OPTION, - JOptionPane.QUESTION_MESSAGE); + JvOptionPane.YES_NO_OPTION, + JvOptionPane.QUESTION_MESSAGE); - if (reply == JOptionPane.YES_OPTION) + if (reply == JvOptionPane.YES_OPTION) { jalview.bin.Cache.log.debug("Opening " + qurl); jalview.util.BrowserLauncher.openURL(qurl); diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java index afb6df4..75ddba5 100644 --- a/src/jalview/gui/VamsasApplication.java +++ b/src/jalview/gui/VamsasApplication.java @@ -174,7 +174,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource } } catch (InvalidSessionDocumentException e) { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, @@ -182,7 +182,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"), MessageManager .getString("label.vamsas_document_import_failed"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } } @@ -665,15 +665,15 @@ public class VamsasApplication implements SelectionSource, VamsasSource { Cache.log .debug("Asking user if the vamsas session should be stored."); - int reply = JOptionPane + int reply = JvOptionPane .showInternalConfirmDialog( Desktop.desktop, "The current VAMSAS session has unsaved data - do you want to save it ?", "VAMSAS Session Shutdown", - JOptionPane.YES_NO_OPTION, - JOptionPane.QUESTION_MESSAGE); + JvOptionPane.YES_NO_OPTION, + JvOptionPane.QUESTION_MESSAGE); - if (reply == JOptionPane.YES_OPTION) + if (reply == JvOptionPane.YES_OPTION) { Cache.log.debug("Prompting for vamsas store filename."); Desktop.instance.vamsasSave_actionPerformed(null); diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java index dd0e6c2..f650807 100644 --- a/src/jalview/gui/WebserviceInfo.java +++ b/src/jalview/gui/WebserviceInfo.java @@ -707,8 +707,8 @@ public class WebserviceInfo extends GWebserviceInfo implements { public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, message, - title, JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, message, + title, JvOptionPane.WARNING_MESSAGE); } }); diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java index c4d215e..17c0760 100644 --- a/src/jalview/gui/WsJobParameters.java +++ b/src/jalview/gui/WsJobParameters.java @@ -61,7 +61,6 @@ import javax.swing.JComboBox; import javax.swing.JDialog; import javax.swing.JFrame; import javax.swing.JLabel; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.JSplitPane; @@ -233,6 +232,7 @@ public class WsJobParameters extends JPanel implements ItemListener, frame.validate(); javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { // jobPanel.setDividerLocation(0.25); @@ -272,6 +272,7 @@ public class WsJobParameters extends JPanel implements ItemListener, new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { update_actionPerformed(e); @@ -283,6 +284,7 @@ public class WsJobParameters extends JPanel implements ItemListener, new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { delete_actionPerformed(e); @@ -294,6 +296,7 @@ public class WsJobParameters extends JPanel implements ItemListener, new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { create_actionPerformed(e); @@ -305,6 +308,7 @@ public class WsJobParameters extends JPanel implements ItemListener, new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { revert_actionPerformed(e); @@ -315,6 +319,7 @@ public class WsJobParameters extends JPanel implements ItemListener, MessageManager.getString("label.start_job_current_settings"), new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { startjob_actionPerformed(e); @@ -325,6 +330,7 @@ public class WsJobParameters extends JPanel implements ItemListener, MessageManager.getString("label.cancel_job_close_dialog"), new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { canceljob_actionPerformed(e); @@ -736,6 +742,7 @@ public class WsJobParameters extends JPanel implements ItemListener, validate(); } + @Override public void argSetModified(Object modifiedElement, boolean b) { if (settingDialog) @@ -827,6 +834,7 @@ public class WsJobParameters extends JPanel implements ItemListener, settingDialog = stn; } + @Override public void refreshParamLayout() { // optsAndparams.setPreferredSize(null); @@ -1113,40 +1121,47 @@ public class WsJobParameters extends JPanel implements ItemListener, jf.addWindowListener(new WindowListener() { + @Override public void windowActivated(WindowEvent e) { // TODO Auto-generated method stub } + @Override public void windowClosed(WindowEvent e) { } + @Override public void windowClosing(WindowEvent e) { thr.interrupt(); } + @Override public void windowDeactivated(WindowEvent e) { // TODO Auto-generated method stub } + @Override public void windowDeiconified(WindowEvent e) { // TODO Auto-generated method stub } + @Override public void windowIconified(WindowEvent e) { // TODO Auto-generated method stub } + @Override public void windowOpened(WindowEvent e) { // TODO Auto-generated method stub @@ -1316,6 +1331,7 @@ public class WsJobParameters extends JPanel implements ItemListener, String curSetName = null; + @Override public void itemStateChanged(ItemEvent e) { if (e.getSource() == setName && e.getStateChange() == e.SELECTED) @@ -1334,6 +1350,7 @@ public class WsJobParameters extends JPanel implements ItemListener, } javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { doPreferenceComboStateChange(setname); @@ -1355,14 +1372,14 @@ public class WsJobParameters extends JPanel implements ItemListener, } settingDialog = true; System.out.println("Prompting to save " + lsetname); - if (javax.swing.JOptionPane + if (JvOptionPane .showConfirmDialog( this, "Parameter set '" + lsetname + "' is modifed, and your changes will be lost.\nReally change preset ?", "Warning: Unsaved Changes", - javax.swing.JOptionPane.OK_CANCEL_OPTION) != JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION) != JvOptionPane.OK_OPTION) { // revert the combobox to the current item settingDialog = true; @@ -1414,6 +1431,7 @@ public class WsJobParameters extends JPanel implements ItemListener, */ String lastDescrText = null; + @Override public void actionPerformed(ActionEvent e) { if (e.getSource() instanceof Component) @@ -1434,12 +1452,13 @@ public class WsJobParameters extends JPanel implements ItemListener, settingDialog = false; javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - JOptionPane.showMessageDialog(ourframe, MessageManager + JvOptionPane.showMessageDialog(ourframe, MessageManager .getString("label.invalid_name_preset_exists"), MessageManager.getString("label.invalid_name"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); @@ -1475,16 +1494,19 @@ public class WsJobParameters extends JPanel implements ItemListener, } } + @Override public void insertUpdate(DocumentEvent e) { checkDescrModified(); } + @Override public void removeUpdate(DocumentEvent e) { checkDescrModified(); } + @Override public void changedUpdate(DocumentEvent e) { checkDescrModified(); diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java index b6a7672..f0487e3 100644 --- a/src/jalview/gui/WsParamSetManager.java +++ b/src/jalview/gui/WsParamSetManager.java @@ -294,9 +294,9 @@ public class WsParamSetManager implements ParamManager File pfile = new File(filename); if (pfile.exists() && pfile.canWrite()) { - if (JOptionPane.showConfirmDialog(Desktop.instance, + if (JvOptionPane.showConfirmDialog(Desktop.instance, "Delete the preset's file, too ?", "Delete User Preset ?", - JOptionPane.OK_CANCEL_OPTION) == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION) == JvOptionPane.OK_OPTION) { pfile.delete(); } diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java index 6ec25b2..165e8f2 100644 --- a/src/jalview/gui/WsPreferences.java +++ b/src/jalview/gui/WsPreferences.java @@ -459,11 +459,11 @@ public class WsPreferences extends GWsPreferences pane12.add(urltf, BorderLayout.EAST); panel.add(pane12, BorderLayout.NORTH); boolean valid = false; - int resp = JOptionPane.CANCEL_OPTION; + int resp = JvOptionPane.CANCEL_OPTION; while (!valid - && (resp = JOptionPane.showInternalConfirmDialog( + && (resp = JvOptionPane.showInternalConfirmDialog( Desktop.desktop, panel, title, - JOptionPane.OK_CANCEL_OPTION)) == JOptionPane.OK_OPTION) + JvOptionPane.OK_CANCEL_OPTION)) == JvOptionPane.OK_OPTION) { try { @@ -480,18 +480,18 @@ public class WsPreferences extends GWsPreferences } catch (Exception e) { valid = false; - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.invalid_url")); } } - if (valid && resp == JOptionPane.OK_OPTION) + if (valid && resp == JvOptionPane.OK_OPTION) { - int validate = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + int validate = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, MessageManager.getString("info.validate_jabaws_server"), MessageManager.getString("label.test_server"), - JOptionPane.YES_NO_OPTION); + JvOptionPane.YES_NO_OPTION); - if (validate == JOptionPane.OK_OPTION) + if (validate == JvOptionPane.OK_OPTION) { if (Jws2Discoverer.testServiceUrl(foo)) { @@ -499,22 +499,22 @@ public class WsPreferences extends GWsPreferences } else { - int opt = JOptionPane + int opt = JvOptionPane .showInternalOptionDialog( Desktop.desktop, "The Server '" + foo.toString() + "' failed validation,\ndo you want to add it anyway? ", "Server Validation Failed", - JOptionPane.YES_NO_OPTION, - JOptionPane.INFORMATION_MESSAGE, null, null, null); - if (opt == JOptionPane.YES_OPTION) + JvOptionPane.YES_NO_OPTION, + JvOptionPane.INFORMATION_MESSAGE, null, null, null); + if (opt == JvOptionPane.YES_OPTION) { return foo.toString(); } else { - JOptionPane + JvOptionPane .showInternalMessageDialog( Desktop.desktop, MessageManager diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index b449d19..becc434 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -33,6 +33,7 @@ import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.Desktop; import jalview.gui.Jalview2XML; +import jalview.gui.JvOptionPane; import jalview.json.binding.biojson.v1.ColourSchemeMapper; import jalview.schemes.ColourSchemeI; import jalview.structure.StructureSelectionManager; @@ -41,7 +42,6 @@ import jalview.util.MessageManager; import java.util.StringTokenizer; import java.util.Vector; -import javax.swing.JOptionPane; import javax.swing.SwingUtilities; public class FileLoader implements Runnable @@ -273,13 +273,13 @@ public class FileLoader implements Runnable + "\" has null or unidentifiable data content!"); if (!Jalview.isHeadlessMode()) { - javax.swing.JOptionPane.showInternalMessageDialog( + JvOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.getString("label.couldnt_read_data") + " in " + file + "\n" + AppletFormatAdapter.SUPPORTED_FORMATS, MessageManager.getString("label.couldnt_read_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } return; } @@ -464,10 +464,10 @@ public class FileLoader implements Runnable @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, errorMessage, MessageManager .getString("label.error_loading_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -491,12 +491,12 @@ public class FileLoader implements Runnable @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog( + JvOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( "label.problems_opening_file", new String[] { file }), MessageManager .getString("label.file_open_error"), - javax.swing.JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -513,12 +513,12 @@ public class FileLoader implements Runnable @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog( + JvOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( "warn.out_of_memory_loading_file", new String[] { file }), MessageManager .getString("label.out_of_memory"), - javax.swing.JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java index 1ea6795..de2c740 100755 --- a/src/jalview/io/JalviewFileChooser.java +++ b/src/jalview/io/JalviewFileChooser.java @@ -21,6 +21,7 @@ ////////////////////////////////////////////////////////////////// package jalview.io; +import jalview.gui.JvOptionPane; import jalview.util.MessageManager; import jalview.util.Platform; @@ -37,7 +38,6 @@ import java.util.Vector; import javax.swing.DefaultListCellRenderer; import javax.swing.JFileChooser; import javax.swing.JList; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JScrollPane; import javax.swing.SpringLayout; @@ -223,12 +223,12 @@ public class JalviewFileChooser extends JFileChooser if ((ret == JalviewFileChooser.APPROVE_OPTION) && getSelectedFile().exists()) { - int confirm = JOptionPane.showConfirmDialog(parent, + int confirm = JvOptionPane.showConfirmDialog(parent, MessageManager.getString("label.overwrite_existing_file"), MessageManager.getString("label.file_already_exists"), - JOptionPane.YES_NO_OPTION); + JvOptionPane.YES_NO_OPTION); - if (confirm != JOptionPane.YES_OPTION) + if (confirm != JvOptionPane.YES_OPTION) { ret = JalviewFileChooser.CANCEL_OPTION; } diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java index 9d9b940..55e72eb 100755 --- a/src/jalview/io/WSWUBlastClient.java +++ b/src/jalview/io/WSWUBlastClient.java @@ -27,6 +27,7 @@ import jalview.datamodel.Sequence; import jalview.gui.AlignmentPanel; import jalview.gui.CutAndPasteTransfer; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.util.MessageManager; import java.util.ArrayList; @@ -35,7 +36,6 @@ import java.util.StringTokenizer; import java.util.Vector; import javax.swing.ImageIcon; -import javax.swing.JOptionPane; import uk.ac.ebi.www.Data; import uk.ac.ebi.www.InputParams; @@ -150,11 +150,11 @@ public class WSWUBlastClient { // This must be outside the run() body as java 1.5 // will not return any value from the OptionPane to the expired thread. - int reply = JOptionPane.showConfirmDialog(Desktop.desktop, + int reply = JvOptionPane.showConfirmDialog(Desktop.desktop, "Automatically update suggested ids?", - "Auto replace sequence ids", JOptionPane.YES_NO_OPTION); + "Auto replace sequence ids", JvOptionPane.YES_NO_OPTION); - if (reply == JOptionPane.YES_OPTION) + if (reply == JvOptionPane.YES_OPTION) { Enumeration keys = suggestedIds.elements(); while (keys.hasMoreElements()) @@ -211,6 +211,7 @@ public class WSWUBlastClient } } + @Override public void run() { while (jobsRunning > 0) @@ -250,6 +251,7 @@ public class WSWUBlastClient this.sequence = sequence; } + @Override public void run() { StartJob(); diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index af8a172..d2cb5a2 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -23,6 +23,7 @@ package jalview.jbgui; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.api.SplitContainerI; import jalview.bin.Cache; +import jalview.gui.JvOptionPane; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; import jalview.schemes.ColourSchemeProperty; @@ -50,7 +51,6 @@ import javax.swing.JLabel; import javax.swing.JMenu; import javax.swing.JMenuBar; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JRadioButtonMenuItem; import javax.swing.JTabbedPane; @@ -314,13 +314,13 @@ public class GAlignFrame extends JInternalFrame { radioItem.removeActionListener(radioItem.getActionListeners()[0]); - int option = JOptionPane.showInternalConfirmDialog( + int option = JvOptionPane.showInternalConfirmDialog( jalview.gui.Desktop.desktop, MessageManager .getString("label.remove_from_default_list"), MessageManager .getString("label.remove_user_defined_colour"), - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) + JvOptionPane.YES_NO_OPTION); + if (option == JvOptionPane.YES_OPTION) { jalview.gui.UserDefinedColours .removeColourFromDefaults(radioItem.getText()); diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java index 2689946..dbce5f3 100755 --- a/src/jalview/jbgui/GSequenceLink.java +++ b/src/jalview/jbgui/GSequenceLink.java @@ -20,6 +20,7 @@ */ package jalview.jbgui; +import jalview.gui.JvOptionPane; import jalview.gui.JvSwingUtils; import jalview.util.MessageManager; import jalview.util.UrlLink; @@ -35,7 +36,6 @@ import java.awt.event.KeyEvent; import javax.swing.BorderFactory; import javax.swing.JLabel; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JTextField; import javax.swing.SwingConstants; @@ -156,10 +156,10 @@ public class GSequenceLink extends Panel return true; } - JOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop, + JvOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop, MessageManager.getString("warn.url_must_contain"), MessageManager.getString("label.invalid_url"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return false; } diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java index 7e069e3..676a4b6 100644 --- a/src/jalview/ws/DasSequenceFeatureFetcher.java +++ b/src/jalview/ws/DasSequenceFeatureFetcher.java @@ -28,6 +28,7 @@ import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.FeatureSettings; +import jalview.gui.JvOptionPane; import jalview.util.DBRefUtils; import jalview.util.MessageManager; import jalview.util.UrlLink; @@ -46,8 +47,6 @@ import java.util.Set; import java.util.StringTokenizer; import java.util.Vector; -import javax.swing.JOptionPane; - import org.biodas.jdas.client.FeaturesClient; import org.biodas.jdas.client.adapters.features.DasGFFAdapter; import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter; @@ -200,21 +199,21 @@ public class DasSequenceFeatureFetcher if (checkDbrefs && refCount < sequences.length && uniprotCount > 0) { - int reply = JOptionPane.YES_OPTION; + int reply = JvOptionPane.YES_OPTION; if (promptFetchDbrefs) { - reply = JOptionPane + reply = JvOptionPane .showInternalConfirmDialog( Desktop.desktop, MessageManager .getString("info.you_want_jalview_to_find_uniprot_accessions"), MessageManager .getString("label.find_uniprot_accession_ids"), - JOptionPane.YES_NO_OPTION, - JOptionPane.QUESTION_MESSAGE); + JvOptionPane.YES_NO_OPTION, + JvOptionPane.QUESTION_MESSAGE); } - if (reply == JOptionPane.YES_OPTION) + if (reply == JvOptionPane.YES_OPTION) { Thread thread = new Thread(new FetchDBRefs()); thread.start(); diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java index 4643119..7258f51 100644 --- a/src/jalview/ws/jws1/Discoverer.java +++ b/src/jalview/ws/jws1/Discoverer.java @@ -20,14 +20,13 @@ */ package jalview.ws.jws1; +import jalview.gui.JvOptionPane; import jalview.util.MessageManager; import java.util.Hashtable; import java.util.StringTokenizer; import java.util.Vector; -import javax.swing.JOptionPane; - import ext.vamsas.IRegistry; import ext.vamsas.IRegistryServiceLocator; import ext.vamsas.RegistryServiceSoapBindingStub; @@ -255,11 +254,11 @@ public class Discoverer implements Runnable { if (jalview.gui.Desktop.desktop != null) { - JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, + JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, MessageManager.getString("label.set_proxy_settings"), MessageManager .getString("label.proxy_authorization_failed"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } else @@ -383,11 +382,13 @@ public class Discoverer implements Runnable /** * creates a new thread to call discoverServices() */ + @Override public void run() { final Discoverer discoverer = this; Thread discoverThread = new Thread() { + @Override public void run() { discoverer.doDiscovery(); diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java index f13672b..2c05386 100644 --- a/src/jalview/ws/jws1/JPredClient.java +++ b/src/jalview/ws/jws1/JPredClient.java @@ -27,6 +27,7 @@ import jalview.datamodel.SeqCigar; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.WebserviceInfo; import jalview.util.MessageManager; @@ -36,7 +37,6 @@ import java.util.Hashtable; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import ext.vamsas.Jpred; import ext.vamsas.JpredServiceLocator; @@ -323,7 +323,7 @@ public class JPredClient extends WS1Client } catch (Exception ex) { - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, MessageManager @@ -332,7 +332,7 @@ public class JPredClient extends WS1Client new String[] { WebServiceName, WsURL }), MessageManager .getString("label.internal_jalview_error"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); wsInfo.setProgressText(MessageManager .formatMessage( "label.secondary_structure_prediction_service_couldnt_be_located", @@ -345,6 +345,7 @@ public class JPredClient extends WS1Client return server; } + @Override public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh, final AlignFrame af) { @@ -352,6 +353,7 @@ public class JPredClient extends WS1Client method.setToolTipText(sh.getEndpointURL()); method.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction(); diff --git a/src/jalview/ws/jws1/MsaWSClient.java b/src/jalview/ws/jws1/MsaWSClient.java index aad72b1..5ea553e 100644 --- a/src/jalview/ws/jws1/MsaWSClient.java +++ b/src/jalview/ws/jws1/MsaWSClient.java @@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.WebserviceInfo; import jalview.util.MessageManager; @@ -32,7 +33,6 @@ import java.awt.event.ActionListener; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import ext.vamsas.MuscleWSServiceLocator; import ext.vamsas.MuscleWSSoapBindingStub; @@ -78,22 +78,22 @@ public class MsaWSClient extends WS1Client alignFrame = _alignFrame; if (!sh.getAbstractName().equals("MsaWS")) { - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.service_called_is_not_msa_service", new String[] { sh.getName() }), MessageManager .getString("label.internal_jalview_error"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } if ((wsInfo = setWebService(sh)) == null) { - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.msa_service_is_unknown", new String[] { sh.getName() }), MessageManager .getString("label.internal_jalview_error"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } diff --git a/src/jalview/ws/jws1/SeqSearchWSClient.java b/src/jalview/ws/jws1/SeqSearchWSClient.java index 7665fec..92d17e8 100644 --- a/src/jalview/ws/jws1/SeqSearchWSClient.java +++ b/src/jalview/ws/jws1/SeqSearchWSClient.java @@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.WebserviceInfo; import jalview.util.MessageManager; @@ -37,7 +38,6 @@ import java.util.Vector; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import ext.vamsas.SeqSearchServiceLocator; import ext.vamsas.SeqSearchServiceSoapBindingStub; @@ -84,23 +84,23 @@ public class SeqSearchWSClient extends WS1Client // name to service client name if (!sh.getAbstractName().equals(this.getServiceActionKey())) { - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage( "label.service_called_is_not_seq_search_service", new String[] { sh.getName() }), MessageManager .getString("label.internal_jalview_error"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } if ((wsInfo = setWebService(sh)) == null) { - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.seq_search_service_is_unknown", new String[] { sh.getName() }), MessageManager .getString("label.internal_jalview_error"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index 8fa118d..b723059 100644 --- a/src/jalview/ws/jws2/MsaWSClient.java +++ b/src/jalview/ws/jws2/MsaWSClient.java @@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.JvSwingUtils; import jalview.util.MessageManager; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -37,7 +38,6 @@ import java.util.List; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.ToolTipManager; import compbio.data.msa.MsaWS; @@ -107,22 +107,22 @@ public class MsaWSClient extends Jws2Client if (!(sh.service instanceof MsaWS)) { // redundant at mo - but may change - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.service_called_is_not_msa_service", new String[] { sh.serviceType }), MessageManager .getString("label.internal_jalview_error"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } server = (MsaWS) sh.service; if ((wsInfo = setWebService(sh, false)) == null) { - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.msa_service_is_unknown", new String[] { sh.serviceType }), MessageManager .getString("label.internal_jalview_error"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -180,10 +180,10 @@ public class MsaWSClient extends Jws2Client } else { - JOptionPane.showMessageDialog(alignFrame, + JvOptionPane.showMessageDialog(alignFrame, MessageManager.getString("info.invalid_msa_input_mininfo"), MessageManager.getString("info.invalid_msa_notenough"), - JOptionPane.INFORMATION_MESSAGE); + JvOptionPane.INFORMATION_MESSAGE); wsInfo.setVisible(false); } } diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index 2af31bb..4702686 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -67,9 +67,9 @@ public class SequenceAnnotationWSClient extends Jws2Client // dan changed! dan test. comment out if conditional // if (alignFrame.getViewport().getAlignment().isNucleotide()) // { - // JOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType + // JvOptionPane.showMessageDialog(Desktop.desktop, sh.serviceType // + " can only be used\nfor amino acid alignments.", - // "Wrong type of sequences!", JOptionPane.WARNING_MESSAGE); + // "Wrong type of sequences!", JvOptionPane.WARNING_MESSAGE); // return; // // } diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java index 1fb9259..7fbae89 100644 --- a/src/jalview/ws/rest/RestClient.java +++ b/src/jalview/ws/rest/RestClient.java @@ -26,6 +26,7 @@ import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.AlignmentPanel; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.WebserviceInfo; import jalview.io.packed.DataProvider.JvDataType; import jalview.util.MessageManager; @@ -40,7 +41,6 @@ import java.util.Vector; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; @@ -324,7 +324,7 @@ public class RestClient extends WSClient implements WSClientI, else { // TODO: try to tell the user why the job couldn't be started. - JOptionPane + JvOptionPane .showMessageDialog( Desktop.desktop, (jobsthread.hasWarnings() ? jobsthread.getWarnings() @@ -332,7 +332,7 @@ public class RestClient extends WSClient implements WSClientI, .getString("label.job_couldnt_be_started_check_input")), MessageManager .getString("label.unable_start_web_service_analysis"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } -- 1.7.10.2