X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9aed70d9cd937e71e11af5ca359010dc21dfd174;hb=b0cee3aaf7d8873910939f97b6acb217d518968d;hp=f31a22033ed6194f03b3a1d6c92d7b243826d5e9;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index f31a220..9aed70d 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -75,7 +75,6 @@ import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.JnetAnnotationMaker; import jalview.io.NewickFile; -import jalview.io.StructureFile; import jalview.io.TCoffeeScoreFile; import jalview.jbgui.GAlignFrame; import jalview.schemes.Blosum62ColourScheme; @@ -88,7 +87,9 @@ import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.RNAHelicesColour; import jalview.schemes.RNAHelicesColourChooser; +import jalview.schemes.ResidueColourScheme; import jalview.schemes.ResidueProperties; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; @@ -126,7 +127,6 @@ import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; -import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.print.PageFormat; import java.awt.print.PrinterJob; @@ -147,8 +147,6 @@ import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; -import javax.swing.JRadioButtonMenuItem; import javax.swing.JScrollPane; import javax.swing.SwingUtilities; @@ -858,14 +856,40 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, conservationMenuItem.setEnabled(!nucleotide); modifyConservation.setEnabled(!nucleotide); showGroupConservation.setEnabled(!nucleotide); + + /* + * enable / disable colour schemes + * - the old, simple way (based on the nucleotide flag), or + * - the new, generic way (interrogate the colour scheme) + */ + AlignmentI al = getViewport().getAlignment(); + clustalColour.setEnabled(!nucleotide); + zappoColour.setEnabled(!nucleotide); + taylorColour.setEnabled(!nucleotide); + hydrophobicityColour.setEnabled(!nucleotide); + helixColour.setEnabled(!nucleotide); + strandColour.setEnabled(!nucleotide); + turnColour.setEnabled(!nucleotide); + // buriedColour.setEnabled(!nucleotide); + // TODO make isApplicableTo static in ColourSchemeI in Java 8 + buriedColour.setEnabled(new BuriedColourScheme().isApplicableTo(al)); rnahelicesColour.setEnabled(nucleotide); - purinePyrimidineColour.setEnabled(nucleotide); + nucleotideColour.setEnabled(nucleotide); + // purinePyrimidineColour.setEnabled(nucleotide); + purinePyrimidineColour.setEnabled(new PurinePyrimidineColourScheme() + .isApplicableTo(al)); + tcoffeeColour + .setEnabled(new TCoffeeColourScheme(al).isApplicableTo(al)); + RNAInteractionColour.setEnabled(nucleotide); showComplementMenuItem.setText(nucleotide ? MessageManager .getString("label.protein") : MessageManager .getString("label.nucleotide")); - setColourSelected(jalview.bin.Cache.getDefault( + + String selectedColourScheme = Cache.getDefault( nucleotide ? Preferences.DEFAULT_COLOUR_NUC - : Preferences.DEFAULT_COLOUR_PROT, "None")); + : Preferences.DEFAULT_COLOUR_PROT, + ResidueColourScheme.NONE); + setColourSelected(selectedColourScheme); } /** @@ -928,7 +952,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, autoCalculate.setSelected(av.autoCalculateConsensus); sortByTree.setSelected(av.sortByTree); listenToViewSelections.setSelected(av.followSelection); - rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure()); + // rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure()); + rnahelicesColour.setEnabled(new RNAHelicesColour(av.getAlignment()) + .isApplicableTo(av.getAlignment())); rnahelicesColour .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); @@ -1114,11 +1140,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void saveAs_actionPerformed(ActionEvent e) { + String format = currentFileFormat == null ? null : currentFileFormat + .toString(); JalviewFileChooser chooser = JalviewFileChooser.forWrite( - Cache.getProperty("LAST_DIRECTORY"), - // AppletFormatAdapter.WRITABLE_EXTENSIONS, - // AppletFormatAdapter.WRITABLE_FNAMES, - currentFileFormat.toString(), false); + Cache.getProperty("LAST_DIRECTORY"), format); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -1132,14 +1157,14 @@ 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) @@ -1235,11 +1260,11 @@ 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; @@ -1254,8 +1279,8 @@ 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; } @@ -2372,13 +2397,13 @@ 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; } @@ -3301,7 +3326,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void textColour_actionPerformed(ActionEvent e) + public void textColour_actionPerformed() { new TextColourChooser().chooseColour(alignPanel, null); } @@ -3313,7 +3338,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed() { changeColour(null); } @@ -3325,7 +3350,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void clustalColour_actionPerformed(ActionEvent e) + public void clustalColour_actionPerformed() { changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences())); @@ -3338,7 +3363,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void zappoColour_actionPerformed(ActionEvent e) + public void zappoColour_actionPerformed() { changeColour(new ZappoColourScheme()); } @@ -3350,7 +3375,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void taylorColour_actionPerformed(ActionEvent e) + public void taylorColour_actionPerformed() { changeColour(new TaylorColourScheme()); } @@ -3362,7 +3387,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void hydrophobicityColour_actionPerformed(ActionEvent e) + public void hydrophobicityColour_actionPerformed() { changeColour(new HydrophobicColourScheme()); } @@ -3374,7 +3399,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void helixColour_actionPerformed(ActionEvent e) + public void helixColour_actionPerformed() { changeColour(new HelixColourScheme()); } @@ -3386,7 +3411,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void strandColour_actionPerformed(ActionEvent e) + public void strandColour_actionPerformed() { changeColour(new StrandColourScheme()); } @@ -3398,7 +3423,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void turnColour_actionPerformed(ActionEvent e) + public void turnColour_actionPerformed() { changeColour(new TurnColourScheme()); } @@ -3410,7 +3435,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void buriedColour_actionPerformed(ActionEvent e) + public void buriedColour_actionPerformed() { changeColour(new BuriedColourScheme()); } @@ -3422,25 +3447,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void nucleotideColour_actionPerformed(ActionEvent e) + public void nucleotideColour_actionPerformed() { changeColour(new NucleotideColourScheme()); } @Override - public void purinePyrimidineColour_actionPerformed(ActionEvent e) + public void purinePyrimidineColour_actionPerformed() { changeColour(new PurinePyrimidineColourScheme()); } /* - * public void covariationColour_actionPerformed(ActionEvent e) { + * public void covariationColour_actionPerformed() { * changeColour(new * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation * ()[0])); } */ @Override - public void annotationColour_actionPerformed(ActionEvent e) + public void annotationColour_actionPerformed() { new AnnotationColourChooser(viewport, alignPanel); } @@ -3452,7 +3477,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } @Override - public void rnahelicesColour_actionPerformed(ActionEvent e) + public void rnahelicesColour_actionPerformed() { new RNAHelicesColourChooser(viewport, alignPanel); } @@ -3460,11 +3485,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! * - * @param e - * DOCUMENT ME! */ @Override - protected void applyToAllGroups_actionPerformed(ActionEvent e) + protected void applyToAllGroups_actionPerformed() { viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); } @@ -3514,7 +3537,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void modifyPID_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed() { if (viewport.getAbovePIDThreshold() && viewport.getGlobalColourScheme() != null) @@ -3532,7 +3555,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void modifyConservation_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { if (viewport.getConservationSelected() && viewport.getGlobalColourScheme() != null) @@ -3550,7 +3573,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { viewport.setConservationSelected(conservationMenuItem.isSelected()); @@ -3559,7 +3582,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, changeColour(viewport.getGlobalColourScheme()); - modifyConservation_actionPerformed(null); + modifyConservation_actionPerformed(); } /** @@ -3569,7 +3592,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void abovePIDThreshold_actionPerformed(ActionEvent e) + public void abovePIDThreshold_actionPerformed() { viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); @@ -3578,7 +3601,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(null); + modifyPID_actionPerformed(); } /** @@ -3597,104 +3620,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - UserColourScheme udc = (UserColourScheme) UserDefinedColours + UserColourScheme udc = UserDefinedColours .getUserColourSchemes().get(e.getActionCommand()); changeColour(udc); } } - public void updateUserColourMenu() - { - - Component[] menuItems = colourMenu.getMenuComponents(); - int iSize = menuItems.length; - for (int i = 0; i < iSize; i++) - { - if (menuItems[i].getName() != null - && menuItems[i].getName().equals("USER_DEFINED")) - { - colourMenu.remove(menuItems[i]); - iSize--; - } - } - if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null) - { - java.util.Enumeration userColours = jalview.gui.UserDefinedColours - .getUserColourSchemes().keys(); - - while (userColours.hasMoreElements()) - { - final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem( - userColours.nextElement().toString()); - radioItem.setName("USER_DEFINED"); - radioItem.addMouseListener(new MouseAdapter() - { - @Override - public void mousePressed(MouseEvent evt) - { - if (evt.isPopupTrigger()) // Mac - { - offerRemoval(radioItem); - } - } - - @Override - public void mouseReleased(MouseEvent evt) - { - if (evt.isPopupTrigger()) // Windows - { - offerRemoval(radioItem); - } - } - - /** - * @param radioItem - */ - void offerRemoval(final JRadioButtonMenuItem radioItem) - { - radioItem.removeActionListener(radioItem.getActionListeners()[0]); - - int option = JOptionPane.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) - { - jalview.gui.UserDefinedColours - .removeColourFromDefaults(radioItem.getText()); - colourMenu.remove(radioItem); - } - else - { - radioItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - } - } - }); - radioItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - userDefinedColour_actionPerformed(evt); - } - }); - - colourMenu.insert(radioItem, 15); - colours.add(radioItem); - } - } - } - /** * DOCUMENT ME! * @@ -3702,7 +3634,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void PIDColour_actionPerformed(ActionEvent e) + public void PIDColour_actionPerformed() { changeColour(new PIDColourScheme()); } @@ -3714,7 +3646,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! */ @Override - public void BLOSUM62Colour_actionPerformed(ActionEvent e) + public void BLOSUM62Colour_actionPerformed() { changeColour(new Blosum62ColourScheme()); } @@ -3809,10 +3741,10 @@ 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 { @@ -3838,14 +3770,14 @@ 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; } @@ -3943,14 +3875,14 @@ 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; } @@ -3961,14 +3893,14 @@ 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; } @@ -3982,14 +3914,14 @@ 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; } @@ -4254,11 +4186,11 @@ 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); } @@ -4334,27 +4266,27 @@ 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); } } } @Override - protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) + protected void tcoffeeColorScheme_actionPerformed() { changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); } @@ -4733,8 +4665,8 @@ 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) @@ -4743,8 +4675,8 @@ 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 { @@ -4899,13 +4831,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { type = null; } - if (type != null) + if (type != null && type.isStructureFile()) { - if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type)) - { - filesmatched.add(new Object[] { file, protocol, mtch }); - continue; - } + filesmatched.add(new Object[] { file, protocol, mtch }); + continue; } } // File wasn't named like one of the sequences or wasn't a PDB file. @@ -4916,7 +4845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (filesmatched.size() > 0) { if (Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS", false) - || JOptionPane + || JvOptionPane .showConfirmDialog( this, MessageManager @@ -4929,7 +4858,7 @@ 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) @@ -4959,7 +4888,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (assocfiles > 0 && (Cache.getDefault( - "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JOptionPane + "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false) || JvOptionPane .showConfirmDialog( this, "" @@ -4974,7 +4903,7 @@ 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; } @@ -5039,7 +4968,7 @@ 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 @@ -5047,7 +4976,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, : tcf.getWarningMessage(), MessageManager .getString("label.problem_reading_tcoffee_score_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } } else @@ -5169,8 +5098,8 @@ 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) { @@ -5842,7 +5771,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs .size()])); - AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, + GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); cdna.alignAs(alignment); String newtitle = "cDNA " + MessageManager.getString("label.for") + " " @@ -5909,12 +5838,12 @@ 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