X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=ca0fb7f24f62570bd016e6cec11d24495f441c91;hb=refs%2Fheads%2Fspike%2FJAL-4047%2FJAL-4048_columns_in_sequenceID;hp=1c3ab8fcbbdd9e5a49240f34d068836704187303;hpb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 1c3ab8f..ca0fb7f 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -20,8 +20,6 @@ */ package jalview.gui; -import java.util.Locale; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.event.ActionEvent; @@ -34,6 +32,7 @@ import java.util.Collections; import java.util.Hashtable; import java.util.LinkedHashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Objects; import java.util.SortedMap; @@ -88,6 +87,8 @@ import jalview.util.Platform; import jalview.util.StringUtils; import jalview.util.UrlLink; import jalview.viewmodel.seqfeatures.FeatureRendererModel; +import jalview.viewmodel.seqfeatures.IdColumn; +import jalview.viewmodel.seqfeatures.IdColumns; /** * The popup menu that is displayed on right-click on a sequence id, or in the @@ -359,14 +360,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } /** - * Constructor for a PopupMenu for a click in the alignment panel (on a residue) + * Constructor for a PopupMenu for a click in the alignment panel (on a + * residue) * * @param ap - * the panel in which the mouse is clicked + * the panel in which the mouse is clicked * @param seq - * the sequence under the mouse + * the sequence under the mouse * @throws NullPointerException - * if seq is null + * if seq is null */ public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column) { @@ -377,13 +379,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * Constructor for a PopupMenu for a click in the sequence id panel * * @param alignPanel - * the panel in which the mouse is clicked + * the panel in which the mouse is clicked * @param seq - * the sequence under the mouse click + * the sequence under the mouse click * @param groupLinks - * templates for sequence external links + * templates for sequence external links * @throws NullPointerException - * if seq is null + * if seq is null */ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq, List groupLinks) @@ -399,11 +401,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * @param alignPanel * @param seq * @param column - * aligned column position (0...) + * aligned column position (0...) * @param groupLinks */ - private PopupMenu(boolean fromIdPanel, - final AlignmentPanel alignPanel, + private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel, final SequenceI seq, final int column, List groupLinks) { Objects.requireNonNull(seq); @@ -443,9 +444,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /* * And repeat for the current selection group (if there is one): */ - final List selectedGroup = (alignPanel.av.getSelectionGroup() == null - ? Collections. emptyList() - : alignPanel.av.getSelectionGroup().getSequences()); + final List selectedGroup = (alignPanel.av + .getSelectionGroup() == null + ? Collections. emptyList() + : alignPanel.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, @@ -671,7 +673,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable<>(), reppdb = new Hashtable<>(); + Hashtable pdbe = new Hashtable<>(), + reppdb = new Hashtable<>(); SequenceI sqass = null; for (SequenceI sq : alignPanel.av.getSequenceSelection()) @@ -708,7 +711,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); - editGroupMenu.setText(MessageManager.getString("action.edit_new_group")); + editGroupMenu + .setText(MessageManager.getString("action.edit_new_group")); } else { @@ -724,9 +728,38 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener rnaStructureMenu.setVisible(false); } + if (forIdPanel) + { + addDisplayColumnsMenu(); + } + addLinksAndFeatures(seq, column); } + void addDisplayColumnsMenu() + { + JMenu dis_cols = new JMenu( + MessageManager.getString("action.displayed_columns")); + final IdColumns id_cols = ap.av.getIdColumns(); + id_cols.updateTypeList(); + for (final IdColumn col : id_cols.getIdColumns()) + { + JMenuItem col_entry = new JCheckBoxMenuItem(col.getLabel(), + col.isVisible()); + col_entry.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + id_cols.toggleVisible(col.getLabel()); + } + }); + dis_cols.add(col_entry); + } + add(dis_cols); + } + /** * Adds *
    @@ -735,8 +768,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener *
  • positional feature links (alignment panel popup menu)
    • *
  • feature details links (alignment panel popup menu)
    • *
- * If this panel is also showed complementary (CDS/protein) features, then links - * to their feature details are also added. + * If this panel is also showed complementary (CDS/protein) features, then + * links to their feature details are also added. * * @param seq * @param column @@ -904,6 +937,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener if (Platform.isJS()) { details = new JInternalFrame(); + details.setFrameIcon(null); JPanel panel = new JPanel(new BorderLayout()); panel.setOpaque(true); panel.setBackground(Color.white); @@ -1144,8 +1178,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener if (((String[]) sarray[1])[sq] == null) { - if (!e.hasMap() || (e.getMap() - .locateMappedRange(start, end) != null)) + if (!e.hasMap() + || (e.getMap().locateMappedRange(start, end) != null)) { ((String[]) sarray[1])[sq] = e.getAccessionId(); ((int[]) sarray[0])[0]++; @@ -1732,10 +1766,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected void addReferenceAnnotations_actionPerformed( Map> candidates) { - final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup(); final AlignmentI alignment = this.ap.getAlignment(); AlignmentUtils.addReferenceAnnotations(candidates, alignment, - selectionGroup); + null); refresh(); } @@ -1784,7 +1817,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } inserts.and(sq.getInsertionsAsBits()); } - hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(), + hidden.clearAndHideColumns(inserts, + ap.av.getSelectionGroup().getStartRes(), ap.av.getSelectionGroup().getEndRes()); } @@ -1813,7 +1847,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener contents.append("

" + MessageManager.formatMessage( "label.create_sequence_details_report_annotation_for", new Object[] - { seq.getDisplayId(true) }) + "

"); + { seq.getDisplayId(true) }) + "

\n

"); new SequenceAnnotationReport(false).createSequenceAnnotationReport( contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("

"); @@ -1832,6 +1866,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener pane.setBackground(Color.WHITE); pane.add(textLabel, BorderLayout.NORTH); frame = new JInternalFrame(); + frame.setFrameIcon(null); frame.getContentPane().add(new JScrollPane(pane)); } else @@ -1983,15 +2018,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener MessageManager.getString("label.group_description")); dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_group_name_description"), - new Runnable() - { - @Override - public void run() - { - sg.setName(dialog.getName()); - sg.setDescription(dialog.getDescription()); - refresh(); - } + () -> { + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); }); } @@ -2014,8 +2044,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /** * Shows a dialog where the sequence name and description may be edited. If a - * name containing spaces is entered, these are converted to underscores, with a - * warning message. + * name containing spaces is entered, these are converted to underscores, with + * a warning message. */ void sequenceName_actionPerformed() { @@ -2023,32 +2053,30 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sequence.getDescription(), MessageManager.getString("label.sequence_name"), MessageManager.getString("label.sequence_description")); - dialog.showDialog(ap.alignFrame, - MessageManager.getString( - "label.edit_sequence_name_description"), - new Runnable() - { - @Override - public void run() + dialog.showDialog(ap.alignFrame, MessageManager + .getString("label.edit_sequence_name_description"), () -> { + if (dialog.getName() != null) { - if (dialog.getName() != null) + if (dialog.getName().indexOf(" ") > -1) { - if (dialog.getName().indexOf(" ") > -1) - { - JvOptionPane.showMessageDialog(ap, - MessageManager.getString( - "label.spaces_converted_to_underscores"), - MessageManager.getString( - "label.no_spaces_allowed_sequence_name"), - JvOptionPane.WARNING_MESSAGE); - } - sequence.setName(dialog.getName().replace(' ', '_')); - ap.paintAlignment(false, false); + String ok = MessageManager.getString("action.ok"); + String cancel = MessageManager.getString("action.cancel"); + String message = MessageManager.getString( + "label.spaces_converted_to_underscores"); + String title = MessageManager.getString( + "label.no_spaces_allowed_sequence_name"); + Object[] options = new Object[] { ok, cancel }; + + JvOptionPane.frameDialog(message, title, + JvOptionPane.WARNING_MESSAGE, null, null, null, + false); } - sequence.setDescription(dialog.getDescription()); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false, false); } + sequence.setDescription(dialog.getDescription()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); }); } @@ -2078,8 +2106,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ protected void outline_actionPerformed() { - String title = MessageManager - .getString("label.select_outline_colour"); + String title = MessageManager.getString("label.select_outline_colour"); ColourChooserListener listener = new ColourChooserListener() { @Override @@ -2089,8 +2116,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener refresh(); } }; - JalviewColourChooser.showColourChooser(Desktop.getDesktop(), - title, Color.BLUE, listener); + JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title, + Color.BLUE, listener); } /** @@ -2195,7 +2222,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener String[] omitHidden = null; - System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens + jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a prompt happens // or we simply trust the user wants // wysiwig behaviour @@ -2271,25 +2298,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null); dialog.showDialog(ap.alignFrame, - MessageManager.getString("label.edit_sequence"), - new Runnable() - { - @Override - public void run() - { - EditCommand editCommand = new EditCommand( - MessageManager.getString("label.edit_sequences"), - Action.REPLACE, - dialog.getName().replace(' ', - ap.av.getGapCharacter()), - sg.getSequencesAsArray( - ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1, - ap.av.getAlignment()); - ap.alignFrame.addHistoryItem(editCommand); - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - } + MessageManager.getString("label.edit_sequence"), () -> { + EditCommand editCommand = new EditCommand( + MessageManager.getString("label.edit_sequences"), + Action.REPLACE, + dialog.getName().replace(' ', + ap.av.getGapCharacter()), + sg.getSequencesAsArray( + ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1, + ap.av.getAlignment()); + ap.alignFrame.addHistoryItem(editCommand); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); }); } }